I've been playing around in the latest version for a bit, and noticed a problem. You don't get many compounds directly after reproduction. You get some, which is fine for small cells, but bigger cells have bigger metabolic requirements which make it harder to start off (just 10 ATP for my 3-toxin vacuole 6-flaggela monster?).
Right now, there's no way to circumvent this: any compounds gathered before reproducing seem to vanish off into the aether, leaving nothing for the newly split cell. To fix this, the compounds available after reproducing should be dependent on those before, perhaps halved.
It's definitely going to be part of the revamped reproductive system in a future update. What is certain is that there will be no RPase, your compound stores will get halved, and you will also spend compounds (such as fatty acids, amino acids, and nucleic acids) duplicating your cell. However, what has yet to be decided is whether you can reproduce only after a certain threshold, or at any time, and whether the cells will grow over time as they consume more compounds. A thread will go up on the development forums on it soon (as in after I finish posting the next round for the forum game, I'm going to post a thread on it).