Greetings,
First off, thanks to the Roll20 team for an amazing, well-built, much needed application. I'm also a developer, so I know it ain't easy creating good, friendly stuff.
On to the actual topic: an in-game, mechanical system. Doesn't have to be specific at all; one generic mode might not do, but one can easily group games that have similar mechanical/game systems.
What I'm getting at is just enhance the token (and perhaps map) relationship.
For example (based loosely on d20/D&D game system): when one token marks another for an attack, you roll for the attack, if it hits, go for a damage roll, if not, then proceed normally. If a damage roll does occur, then subtract the total to the HP of the monster (defacto HP bar for me is Bar1-green). Also, be able to associate PCs with their respective Tokens.
That is, IMHO, pretty generic. Sure, if you wanna go ahead and state in the macro that the attack has an effect and if the attack hits, the token hit by the attack gets a red dot indicating that condition, icing on the cake! But that may be too specific or too much work for the devs at this point.
You can also play around with that idea: enable Macros to hold effects, make PC's move only certain amount of squares-dictated by their speed (can be placed in Character info), let terrain come into play when you're creating the map (ie: set terrain as difficult), etc.
Basing it on generic game mechanics, you can take this already amazing tool one-step further, without specializing too much ( in terms of specific gaming systems).
This might not be what the devteam is trying to do with this product, and I can understand that; there are plenty of tools that already accomplish this, but if you can somehow set up modes for different types of games (not just the classical D&D, Shadowrun, etc), then not only can it have the functionality of the already expected campaign manager, but also tap into a niche that will greatly benefit many players. Either way, just wanted to throw it out there since I think it'd be neat and it'd seem like a possible/plausible next step.
If this idea has already been posted, pay me no mind and I'm sorry.
Cheers!