A species forking system would be interesting, but not that important. It could be left optional, or evaluated only on user command.
I think there should not be specifically assigned veggies, but instead just bots with their body consisting largely of chlorophyll. This has been the single most important feature I've been waiting for in DB3. No more zerosims with complicated feeder shepherds, they can now take care of themselves and still evolve to animals! Chloro, on the other hand, should have some kinds of movement slowing/shot weakening/other downsides, to prevent veggyism from becoming the automatic best solution.
An in-sim DNA editor would definitely be helpful, so that one wouldn't have to constantly reload a sim when tweaking with a bot. As of DNA visibility, it could be done pretty much like it's now: the DNA itself is invisible, but certain aspects of it can be seen through ref-sysvars.
DNA should be quite flexible, allowing complicated structures and maybe some obscure stack manipulation (stacks are preserved betweed codules, perhaps?). But, on the other hand, the sysvars need to be redesigned so that an exact value is seldom needed for a task. If shooting is implemented, it should be broken into as many sysvars as there are shot types, for example. This way, mutations on the control flow and conditional structures could be dramatic, but changing numbers little by little probably wouldn't.