When you get round to fixing the UI for conditionals how about adding a 'library' facility.
This would allow a user to build up a conditional set of rules that could be 'parked' ready to apply en-masse to a given game (I'm thinking here of creating multiple "libraries" for a different openings mostly).
If you get the set up right, you could use this for the themed tournaments (a library for white and a library for black until the agreed point) and then everyone could have fully working PGNs that don't have to be edited (You could 'lock' these games until the library had run its course so the openings don't get mucked up by the 'eager'
It would be really nice if you could create library (all the white moves for example) from an existing game (finishing at a pre-determined point). It would then be possible to create rated 'set-piece' games that actually start from move 1 but play through all the moves "automagically" until the agreed point (both players would have to set the game to be just so).
Another requested feature would be a timed response. Instead of the current timing before a conditional kicks in, allow the user to stipulate a time to wait before the conditional should be played. If I'm going to be away for a while, but I've put in the time to think carefully about my moves, then why make what looks like an "instant" response? Maybe this time could be expressed as a percentage of timeout?