From another thread "Also, the cell still stockpiles CO2, which sometimes kill you since you don't have any room for oxygen, so keep that in mind."
Under the threshold system, there is a low threshold where the microbe will try to absorb compounds, a high threshold above which it will try to use up compounds and a vent threshold above which the microbe will just vent the excess instantaneously. This means stockpiling is no longer a problem as each compound has it's own set of thresholds.
The problem this raises, however, is how to relate the thresholds to one another. Say you add a vacuole what effect should that have? Should it increase all your thresholds for all compounds? Should you be able to choose a specific compound for it to store?
Normally it really doesn't matter what your thresholds are because compounds are just passing through the bins as they are processed and storage isn't really important. However it is very important during a period when a resource is scarce. Maybe there is a day night cycle or maybe there are periodic bacterial blooms which use up all of one compound. In these cases what you are storing, and how much of it you have, becomes very important.
Edit: @seregon will hate this because it's discontinuous but...
We could have a low vent threshold and a high vent threshold. When the level of the compound gets to the high threshold it instantly vents down to the level of the low threshold. Obviously disgustingly discontinuous but it would work really well with the compound clouds because the microbes would produce a reasonable sized cloud every once in a while rather than trying to produce a little cloud every timestep.
I suppose in the CPA system the release could be spread out over time to get the continuity back whereas in the swimming around it could be instant.