I think we should ban the Cloner and just go with the other 7 skills on this thread. I think the idea of going over the 100% mark is just ridiculous, and plus, we should really be thinking of a literally ground-breaking skill, such as a fencer, laser or maybe even a blow-torcher (Like the one in the Worms games).
It's not unprecedented; the PS3 version has something just like the Cloner, except it's an object rather than a skill (and doesn't turn the clone around). But there are (for example) a level that has 20 lemmings and requires saving 21 (it doesn't use percentages on that version).
My reason for not going with a ground-breaking tool is that ultimately, while it woudl be beneficial to this topic, it probably wouldn't be so beneficial in general. The Cloner is a very new concept; much more so that a destructive skill in a slightly different direction. That's what the addition of a skill needs to take into account - what kind of potential it adds to new levels. Indeed, I've already thought of (though not made) a few interesting ideas for levels using this one; whereas so far, aside from the stroke of genius I had with Stone Hot Sacrifice, I haven't really come up with anything overly great for the rest, unless it's in combination with the Cloner - and even SHS, for example, some of the skills don't really add anything to the puzzle except being there for the sake of using them (and maybe teaching a new idea about them) - for example, the water could be removed removing the need for both the Stoner and the Swimmer; a wall could be placed to remove one of the walkers, etc.
Obviously, Challenge Mode does encourage doing that on challenges that don't specifically prohibit it or give higher priority to something else (such as fewest skills used).
One option I could consider adding in the next update - though I'm not sure how exactly this would work together with Challenge Mode - is adding a third option alongside "use percent" or "use lemming count", which would be "use cloner-adjusted percents" - basically, the percent values would be based off the number of lemmings plus the number of cloners, so that saving every lemming with all cloners used would equal 100%. Needless to say this would just be a cosmetic thing - in fact, percentages already are purely cosmetic in NeoLemmix; behind-the-scenes it works off the lemming count (unlike traditional which does indeed work off the percentages directly - for example, if you make a level with 200 lemmings and set the save requirement at 199, you'll still pass if you save 198, because that's still equal to 99% - this is part of what enables the nuke glitch).