ah yes now I remember vaguely, this freeze time function.... One has to wonder; why not just make pause behave this way? Why have essentially two different types of pause buttons?? Can't it do everything freeze time can, including incurring the penalty, without *failing to pause*?

No they can't be merged [edit: well maybe see below], because the two pauses serve different functions. The original pause was for actual legit pausing which shouldn't incur any penalty (initial level overview, phone ringing, bathroom break, dinner burning, etc) but we found this could be abused to get higher leaderboard scores, especially on larger (wider) levels by eliminating scrolling time and morph-click accuracy, which would ultimately lead to all high-level players being forced to abuse pause just to have a chance to get the #1 spot, because it would certainly be exploited. I didn't think that was a good direction for competitive play, so we added a few seconds of "recharge" to that pause which shouldn't be an issue for regular pause use and would prevent "cheating".
However I did appreciate that exploiting pause can make the level easier and perhaps more fun for non-competitive players, and so we added "Freeze Time" to encourage that and even allowed giving morphs while time was frozen to lean into that use case. 
Although.... in thinking about it just now I wonder if we could have auto-transitioned from one to the other silently behind the scenes.. so that pausing a few seconds apart would not incur a penalty but pausing any quicker than that would. But giving morphs while paused was only allowed in one not the other so not sure.. hmm..

The other major roadblock was how you assign skills. NeoLemmix has a similar "follow lemming" feature, but as a side option. Selecting a skill then selecting the target lemming just seems to work better most of the time. Especially if you're new to the game and clones may often be spilling out in different directions suddenly you didn't intend, you want to click quickly to get them under control. From being a lemmings player this just felt totally backwards.

Yes Simon had the same thought during beta (gamma?) testing and we implemented a "Morph On Click" option in the Options menu that allows for this.  In that mode you select a morph first (keyboard or click) and then click on a clone to give the action right away.  The reason we reversed this by default was because Clones started as a multiplayer game and in that use case it's more common to want to select a single clone and then issue a bunch of morphs in quick succession, i.e. a sabotage or pathfinding clone lone wolf, possibly wearing a cool decoration   Also by selecting the clone first you can be sure which clone you are going to give the action to, which can be important due to there being dark clones and light clones, "fistfight" game mode, or clones with 2x speed, or tiny/large clones or clones at different gravities (4 ways). I feel selecting the clone first enables better multiplayer success, but the option is there so everyone can choose their preference.

The other issue I can't recall very well but had something to do with physics and how clones moved around. Maybe it was just another issue of differences from being a Lemming player.

Yes the clones are a bit bulky. Originally they started out as thin grey aliens but they chubbed up when the graphics was outsourced. The Light clones are directly controllable like a mario character, but due to the pixel-perfect nature of clones/lemmings they walk a bit odd sometimes. It did take great programming effort to get them to walk on rotating/moving land but I was satisfied with the result and the flexibility of the level editor in general. Moving land can give momentum to clones or crush them allowing for a lot of level design possibilities.  I think it was CCX that created a working minesweeper mini game level, which really impressed me!

Light clone: https://drive.google.com/file/d/1Zta4JI3T0xQJN8QFVA6n-n-VzP3FWRDg/view

I was just watching my step-son play Quantum Connection the other day and we saw the leaderboards had a 5 morph solution which seemed impossible, but after some thinking we figured out how they were doing it!  It's an exploit of the entangled clones where you give a morph to a falling clone that they can't do so they queue it up, but meanwhile the entangled clone performs the morph, then you cancel the morph on the first clone before they hit the ground so they never actually use the morph so it doesn't get counted. Not sure how the top 3 players on that map figured that out but kudos to them!
The leaderboards have never been reset so it's gotten increasingly difficult over the years to get #1 on any level.

Thanks!  Yes the Clones multiplayer is active, but almost all players are first-timers from Steam and very inexperienced (http://clonesgame.com/clonestats/multiplayer/match_history).  I'll grab the latest Lix and try to co-ordinate a time!

We are giving away 1,000 copies of Clones (on Steam) - enter to win one here http://www.steamgifts.com/giveaway/eUW3z/clones

The giveaway lasts until this Saturday the 8th.

In addition, we are having a multiplayer jam this weekend so look for a server or host one at noon CST on Saturday if you are interested     You'd don't even need the full version, the free demo will work! (for limited maps)

I still need to get this... but I think I'll wait until multiplayer picks up a bit, if it's not doing so well right now...

The multiplayer has increased recently, especially in the mornings here (10am CST, early evening over the pond).  We released a patch with multiplayer server notification and in-game package downloading.  The latest level pack by Haymanizer is quite good, i enjoyed it and i suspect other puzzle lovers would too (looking at CCX)

We are giving away free copies of Clones for the upcoming LAN tournament and although online competitors are not likely to be permitted i thought some of you might appreciate the free lunch   To redeem simply enter the coupon "BASELAN22" and click "Apply To Order" when you go through the Clones Store checkout.  If you do take advantage of this then consider uploading a level pack as a way to say thanks.

If the above link does not work for you then just go to http://www.ClonesGame.com and click the "Buy Now" link next to the Clones Store option in the list of distributors.

I'll add that, regardless of what's been said so far about map types and their strategic value, what I like most when playing is variety. I've noticed that geoo and Simon like to stick to their dozen or so favourite maps, and immediately launch into a new game on the same map when they finish. My preference is to play as many different maps as possible, even mediocre ones, just to keep things fresh. Plus, as mentioned alrady, type 2 maps especially are quite demanding on the players, so it's nice to break from those after a while.

I tend to favour playing the same map multiple times as well, in an attempt to find a different and hopefully better strategy.  But map jumping is also fun especially if it's a 2 vs. 2 setup, and nobody has played the new maps yet.  I've recently posted a Clones map pack, you can read a synopsis here with links to screenshots.

Optimal hotkey layout is important for keyboard health.  Having a keyboard for feet would be nice, i'm sure i could hit at least 2 distinct keys per foot with big toe heel pivot.  Hooking up a drum kit as a gaming input device is how we will "play" games in the future.

but I think for me, I can really only work well when given mostly straight-edge terrain pieces, like what you're seeing in Simon's screenshots.

In each of the themed graphics sets in clones there is a folder named "Tiles" which contains mostly square/rectangular terrain.  I tend to like straight edge design also, for gameplay reasons, but the curvy land chunks can look more natural.  It depends what kind of level you want to make.

Interesting thread, allow me to add in my point of view.  My introduction to Lemmings was on the SNES, which included a 2P mode that provided countless hours of exciting competitive chaos.  Clones was an attempt to recreate and expand that feeling.
When designing the MP levels i reviewed all of the SNES ones as well as levels from Pingus to try and get an idea for different categories of levels.  Most obvious grouping was symmetric vs. asymmetric.  The level "Buddy" is an asymmetric map based on a lemmings map where both groups must take the same path the exit, differing only at the very end.  There is an inherent advantage for one player based on the start point positions so noting that i created "Unfair" which attempts to balance the position advantage with a morph count disadvantage.  That map was fun to play, for a time, but after becoming skilled in sabotage it became difficult to counter, although you can always adjust the number of clones/morphs to compensate during the match.  This is why we tweaked the gameplay a bit to try and make sabotage clones less powerful: spinning clone can be shattered, molders can build with no land under them, doppels can be shattered.  I find this makes sabotage easier to deal with, and i am open to further tweaks.
But this leads to the next observation for all symmetrical levels, i believe they are all "type 1" (geoo's classification) in that the goal of MP levels is to win by attacking your opponents path, and thus defending your own constantly.  We tried making maps with no interaction such that the player that makes the best route to their exit first wins, but that was boring (genesis of Multiverse Match mode) so sabotage clones were added.  When in the level the attacking will occur can be delayed for taste by forcing route building or a maze but sabotage is the defining element of MP and once it starts then that becomes the object for the rest of the match if you intent is to win.  The guidelines i tried to follow for creating maps were: allow multiple paths to the exit, use swap traps, force paths to cross, and discourage drilling under start/end points.  Of course some levels break these for variety, but typically if the paths don't cross and there is only one path to the exit it's a boring level.  Recently more maps are incorporating dynamic elements such as moving starts/exits, and modified intent with other game modes such as hiding the identity of a star clone in Capture the Clone mode so that it is only revealed if a dark clone is nearby.  For a true type 3 map i think the goal of the level must not be "who can save more" but a new experimental objective.  The categories of symmetrical level design are broadly just running through all permutations: paths cross above/below starts/exits, cross early/late, inside -> out or outside -> in, multiple starts/extis, and in clones the gravities can multiple these, but if they are the "classic" mode (Corral The Clone) then i'd call them type 1.  Arguably of the most fun Clones maps of this mode is "Lurk" which is small with paths crossing below and almost no route building required.
On the topic of co-op there are 3 kinds: 1) Puzzle co-op in which all players are controlling the same group and working together to complete the level, 2) Puzzle co-op in which each player controls a different group with different abilities (Super Synergy / Quantum Loop) and each group must use its morphs at the right time, and 3) Multiplayer co-op in which each opposing group has multiple players within the group.  I found that #1 was much for fun than i thought it would be, and #3 only works if players within a group are of the same skill level and work together.