Electrical impulses would be the next logical step up from chemical gradients, but I'll settle for just the switchable ties, eh?
In other words, now for the ramble to get some more ideas into circulation:
-About species forking, I don't think too much time should be spent developing a system to handle this. The definition of species is pretty patchy and subjective anyway.
-Mutations can't really be improved, but I would suggest something a little more radical - a type of mutation that would fragment a piece of the DNA and eject it as a virus. This mutation should be extremely uncommon, as it could have a significantly larger effect on an environment.
-Regarding viruses, is it possible to have them accumulate inside a bot until fired or the bot dies? This would be a little more realistic and would make them that much more interesting.
-This is mostly just a detail, but I'm bursting with ideas that will be lost in a few seconds (I had one a second ago that was awesome, but I already forgot)-can enough pressure in the right spot destroy ties? The only real application would be for 'chewing' bits off your prey.
-I heard talk about this before, but I may as well bring it up again-is it possible to have shots that do not directly siphon energy, but rather weaken the cell wall, eventually spilling out the contents of the cell? If so, this shot should probably replace the body shot. This could, in turn, lead to all sorts of different paths. For example, the shots could be modified to either damage the wall immediately, erode it over time, gnaw away on any shells or prevent it from healing, to name a few. Cell walls could be reinforced or protected with a shell; larger bots would have a weaker shell, and more shell would allow less cell growth.
-For senses such as touch, another way of detecting such things is instead of detecting the angle, the cell uses areas (north, west etc.) to determine roughly where it came from, which would encourage MB behavior without making it impossible for bacteria to use these features, and compensate by measuring the magnitude of impact as well?
Sorry about the rambly post, I hope you got at least one useful idea out of it