Well I've been messing around with it. It seems to be the amount of files. I'm still not sure if it's size or number, but its definitely not a specific file.
I've also tried going through and deleting things from each PK3 that I don't want or use like bot files and those sorts of things, and combined a few of them, like putting all Obi-Wan models in the same pk3.
I have 18 PK3's total, besides the assets. 12 of them are just models/skins and the rest are personal mods/tweaks. The total size of all them total is 102 MB.
Does anyone else running the Mac App Store version have this issue?