I've been thinking about that idea for 2.00, but haven't decided for sure if I want to go for it yet. Yes, pickup skill graphics can differ between tilesets (although current graphic sets only have them differ in terms of the border / background colors of the icon). See examples:
http://neolemmix.com/old/levelimg/lpiii/0211.png (Circuit set)
http://neolemmix.com/old/levelimg/lpiv/0311.png (Clockwork set)
I'm not entirely sure about mix-and-match; it's probably doable (though will mean overhauling the level format yet again - but if done at the same time as a move to 2.00n, and - goes without saying - the old format is at least loadable - then it might be viable). Having a "default" raises questions of how it should interact with a loaded one - eg. are the default objects always available as alternative choices? Or are they ignored if the loaded graphic set contains an object of the same type? Etc
There's actually a fair few things that, while doing a major re-code anyway, I'd like to overhaul how they're handled (another one is one-way walls being treated as objects, whereas I quite like how Cheapo does them - they're treated more similarly to steel areas; NeoLemmix currently
supports this but as more of a secondary option, and with limitations (eg. one-way walls done this way will display arrows, but said arrows will not be animated)).