Guest, that last suggestion could get VERY confusing. It could render certain areas completely dark, so you can't even see the lemmings.
I guess I should have joined this discussion sooner! But anyway, a few thoughts:
About multi-style levels: Wouldn't it be simpler just having separate files for the different elements? Example: Having a graphics set file, with just the terrain and the interactive objects, and a lemmings graphics library, with only information about the character animations, and a sound library, which defines a sound effects theme for events. When creating a level, you could simply load these files individually, rather than linking one element with another in a theme. Then, when loading the level, the game would only load the elements used in that level, and not every element associated with every theme used.
For the ancient topic of the technicalities of on-way terrain: It should be fully penetrable, including by bombing, but only by lemmings walking or facing (if they're a blocker) in that direction.
As for giving the position of a bomber five seconds before it explodes; this would be completely impossible without giving many false readings. For example, what if the lemming is in a tunnel being bashed? Will the game take into account the fact that in five seconds, the lemming will be in a newly created area? Or what if within those five seconds you stop the basher, or make him dig? Or what if you put a blocker right in front of the bomber, or make him a blocker? The game can't predict what you will do within those five seconds to alter the bomber's course. And some levels require a bit of skill in timing bombers well, so this feature, even when it's accurate, might spoil some levels. I'd certainly turn the feature off.
About warning when you have too few lemmings to pass the level: Definitely not a message box, but maybe a small line of text in a corner of the screen, which can be turned off in the options screen/box.
About missions: How would the level designer actually define when the mission is complete? It sounds like it would require a lot of programming. Wouldn't it be simpler just designing levels where you need to complete the 'mission' to save the lemmings?
About skills you can pick up: Great idea! But I agree they should be available to all lemmings in that level. Otherwise, you\d need a way of distinguishing which skills are free-for-all and which belong to certain lemmings in the box at the bottom of the screen, and I can't imagine how this would work.
About up and down one-way walls: Does that mean a down one-way wall can only be dug by a lemming the right way up, and an up one-way wall can only be dug by an upside-down lemming, but they can both be bashed in either direction?
I also have a suggestion:
This is a bit of a long-shot, and I'm not sure how easily it could be programmed. How about repeating levels, like in Lemmings Revolution? Not 3D, but where the level and all the lemmings repeat their pattern to infinity, so you can scroll a level with no edges. This can be applied horizontally or vertically, or both. And it can obviously be turned on or off by the level designer. This could also afford many possibilities.
I may have more later.