Hmm... W/ 88 pages of comments, I don't know what's been suggested already. It would be nice to have a summary showing what's already been suggested, and whether it's accepted/rejected/under-consideration/maybe-in-the-future/etc. (also any timeline information would be good too)
But anyway, the suggestions I have are
1) signal vias (like on pc boards) -- allow joining wires of different colors (basically just a post that connects all signal layers) -- this will help a lot w/ the issues of wanting more wire colors...
2) signal diodes -- prevent signal backflow -- an or gate can probably be used for this, but may something explicitly small -- perhaps a 1x2 item which is a diode "stack", ie, red,green,blue,yellow go in one end and come out the other each independantly w/out mixing.
3) one-shot timers -- propagate a pulse after a delay, but don't repeat (should be possible to build this w/ timers and gates, but it ought to be a small, primitive part)
4) sensors of various sorts: a) detect water/liquid; b) detect if a block w/ activator is on or off; -- not sure exactly how this should work as signals are pulses, not on/off. Maybe you send a pulse in, and it either goes thru or not depending on the sensor state?