Erm. May I say something? If not, then tough. :P
Anyway... I think that we need simplicity. Variability, but simplicity.
And I personally think it wouldn't be much of an improvement to make enzymes automatic.
If real organisms actually create enzymes automatically, without any influence from their DNA, then I'd be rather surprised, as well.
Personally, I think digestion should be handled by genes. So what if all the bots go obsolete? Have you seen how pathetic I Flamma is? When I first got this program, I was amazed by how dangerous it was, but now it's sorta crappy.
And also, we are going from 2.35 to 3.0, which is a rather large jump. Either way, bots'll become rather obsolete.
Even my two uberfied bots Duo Minimalis and Deathgrip, will probably need to be rewritten!
Anyway, I'd much rather like it if DNA handled digestion. It'd put more challenge into it!
And also, other then making it a bit easier to program (and I don't think it'd be that much harder to make digestion manual), what advantages do automatic enzymes have?
I don't even think it's really lifelike.
Now, if you propose that we do some kind of system where a bot gets up to 10 enzymes, which their DNA can control, but can't modify, that'd be pretty neat.
In fact, that's not a bad idea.