My only concern is removing potentially complex strategies from being valid. Imagine a bot species that gangs up in the first 100 cycles specifically so it can destroy the opposition before it gains a foot hold.
Or imagine the difference in strategy between PY's praetor bot and Ymir. Usually it ends up being Ymir vs. about 300 Praetor. Yet (at least when Ymir was made) Ymir would always win.
I would cut veg's starting nrg to, say, 1/4 of what it is now, and place down 4 times as many vegs. Then, when vegs repop, repop them with the current nrg settings. I think that should help alleviate any inequitable starting conditions slightly.