What would I change? The pump and the quarry. They're both too cheap (subjective opinion regarding gameplay balance) and too laggy (objective observation regarding Minecraft's handling of flowing liquids). The Extra Utilities version of these items exist for these very reasons. I'm not sure how you'd solve the lag problem without using block replacement, but there's really no reason not to use that method, as far as I can see. Obviously, a more expensive recipe (toggle cheap/expensive in the config, if you must) is simple; I'd probably avoid Ender Pearls
Another issue I've always had with BC appears to be already solved (possibly for a long time). Noticed in the config file the line "
# the lifespan in ticks of items dropped on the ground by pipes and machines, vanilla = 6000, default = 1200
I:itemLifespan=1200"
If, as I assume, setting itemLifespan=0 means dropped items are deleted instantly, that solves one concern. Thousands of items spewing on the ground shouldn't ever be a possibility, certainly not on a server.
As an aside, as I don't really care much: if the Filler drops blocks, how is it not just a quarry with extra features?