Yeah, I mean obviously I realize it's a pretty serious undertaking (I've looked at the game source. It's a little bit less impenetrable than NetHack, but still a lot to do over from scratch), but there are a few other advantages that come with redoing the game engine. Someone mentioned logging messages earlier and how it would be difficult to implement at this stage in the game's design - but that kind of thing is trivially easy to do if you build it into your engine from the beginning. Likewise there's a bunch of interface stuff that would be lovely to have redesigned but that would be such a pain in the ass to do with the current source as to not be worth the trouble. Plus it just seems like it would make a good portable game - it's easy to play in quick bites like a short subway ride, but equally good for longer stretches of time.
...That does remind me of something I meant to suggest that would probably be a lot easier to implement, though. Can you have it set up so that if you have a squad Go Forth, they remember what they were assigned to do before then, and automatically pick it up again the next day (or the next time they're available if you take them out again)? It's a pain to have to go back into the Activate screen every time I send a squad out to do something, even if it's just sending them out to buy clothes/tools. There are naturally some situations where you might not want them to resume what they were doing before (having someone wanted for murder going out and protesting is not a good idea), but it's simple enough to quickly clear someone's tasks, and it's more often that you'd want them to keep doing their original task than you'd want to clear it, anyway, so that should be the default.
Actually maybe I should just make a separate "Interface ideas" thread, since typing this up has reminded me of a few other things that would be handy and wouldn't be much work to implement.