Key among them, when one of the Bot-giving bonuses is in effect, especially "Mega Bot Start", the "deconstruction time to live"/"Entities will place ghosts when destroyed" shouldn't be reset/should be a persistent bonus from the purchase of those, much like the red science milestone and electricity researches are.
Additionally, but as part of a different thing: The Hand size Bonus should also work on Bulk and Stack Inserters, as until level 4 of research, a purple tech, bulk and stack inserters are considerably worse than fast inserters, and that just doesn't feel right.
The utility package purchase should prevent the requirement of crafting a lab to get red science. In fact, the majority, if not all, early trigger techs should be FULLY bypassed once far enough in the prestige tree (which isn't very far as things stand). I'm sure you can understand what I mean and why.
Challenges should scale further (if possible), because I really haven't noticed a speed increase of evolution or more aggressive attacks and expansions.
Resource adjustments should go all the way to 600, and over, if possible with mods.
The Vulcanus Start package is currently non-refundable, even before actual use, so you can't plan around with maybe getting it or not.
Potential "Endless" upgrades: weapon damage, either only personal or the full suite. Player Health. Bot speed, make the early bot start not quite as bad AND allow for ludicrous levels of function (characteristic of a prestige system) without first building an actual megabase.
Alright, I think that's all I can think of to make the comment worth it today.