Been thinking about this some more, and I think this shrould be part of a sort of "next generation" bot programming language.
Basically, I'd have sysvars all be commands. Evolution works best on the stack from my experience. We'd just need to be sure the bots can mutate the different commands.
Each codule could then be given a small private "static memory space", which is entirely protected from other codules, which can be used for long term memory. The root codule's memory space could be entirely copied into children, like racial memory. This private memory space wouldn't need to be very large, maybe on the order of 30 memory locations.
This would entirely change the current ability to "make" another bot do something with ties or shots, though, which I don't think is necessarily a good thing. On the other hand, evolved DNA would be moderately more readable, since it would always be obvious what's being read/written to/from.
I'd vote to keep the old language around, and have bot DNA files specify that they're using the new paradigm. If things don't work out, we're not really out anything. You could even run two species using different paradigms in the same simulation.