Proto pilots need a black hole of resources for life support and PM maintenance.
This keeps getting repeated, but there's nothing in canon that substantiates it. And the fact that the resource-poor Blood Spirits, among many other Clans who aren't exactly rolling in material wealth, were able to not only make Protos work but innovate with them kind of makes the opposite case. Plus, as has already been noted, the Scorpions
aren't strapped for resources, so this doesn't even matter to begin with.
In the Scorpions' case, the only reason they aren't still fielding Protos is because their current writer personally dislikes them and consequently went to great lengths to remove them from the faction using flimsy-at-best logic. I know these forums enjoy trying to headcanon themselves in-universe reasons to account for out-of-universe decisions, but let's be intellectually honest and just call a spade a spade here.
Personally speaking, I think removing Protos from one of the only three active factions that has them (not counting the Home Clans for obvious reasons) was a bad decision. Taking away player options will never sit well with me, when the alternative could've been "if you don't like 'em, don't use 'em". Especially in the context of the Scorpions literally throwing everything but the kitchen sink into the field these days.
Besides, if the Scorpions were able to magically conjure up (read: author fiat) working HPGs in an era that's literally been defined by
no one having them, I don't see why they couldn't just magically conjure up a solution to the side effects of long-term EI implantation. All it would take would be Scorpion scientists refining the Spirits' ProtoMechWarrior phenotype and voila, problem solved. Took me two seconds to come up with that.