That sounds reasonable; I think that the rate at which a cell can change its substance should slowly decrease over time.
About the shell, at the moment it looks like there is three ways of doing it: Make the shell out of nothing (no change), digest minerals that are then used to build a shell, or make minerals structures that can be loosened from or fastened to other minerals to manipulate the shape of the environment into a shell, which can then be used as a sort of communal shell.
More as an idea to throw back in, I still think that a cell wall for retaining energy and keeping the bot intact is worth thinking about. Could make for some pressure interactions as well, as currently 'chewing' is impossible to simulate and invariably results in the prey shooting right back out.
You have a good point; the processing power this might require, however, at first frightens me. There could be a few ways to do it: 1) little particles in a bot bounce around, and if they go fast enough, they fly through the cell wall. 2) standard pressure calculations to determine if a bot is about to "Explode"
These two possibilities have complimentary, almost opposite downsides.
1) this is memory intensive, and possibly also slightly processing intensive.
2) this is process intensive, and depending on if shape is accounted for, could be slightly memory intensive.
Now, I know a few complicated algorithms might be able to remedy this to a degree, but in the end, it would have a huge effect on the speed of the simulation.
To put it into perspective, I believe the goal is to have it run reasonably fast at about 1,000 bots, which in DB2 is just a pipe dream. Every cycle, assuming 1,000 bots, the system would have to execute 1,000 DNA's, update 1,000 bots, process the velocity, acceleration, inertia, momentum, rotation, collisions, and torque of at LEAST 1,000 objects; all that, and to make the speed reasonable, do it about 15-30 times every SECOND.
As you can see, every little thing you add in has an effect on how much the computer has to do, so adding even just 10 particles of energy per bot would greatly influence the speed. Looking at it this way, it is possible to use technique 2, but the math is tricky, and if we run into any trig we might as well just forget about it, because computers and trig are not good buddies