Psi balance for base defense

[Alpha Centauri Bear]

The biggest problem with popped units is not that it is difficult to fight them and not even that they kill units in bases but that they destroy improvements at incredible rate (along with fungus covering everything). That alone turns land into an unusable desert which has an enormous impact at end game. That alone is a major AI weakness already as many pointed out. It just stops developing and die by itself if human player survives until then.

[Nexii]

I think it's fine to have intrinsic base defense vs PSI. The boost for bases never seemed like too much of a stretch given the Children's Creche lore.

I have been trying out Rover speed worms with 50% base defense. They are less of a threat to bases but a lot more scary out in the field.

As for late-game fungal pop mechanics, you could try boosting up the production on fungus tiles. Fungus isn't much of a consideration in the stock game as a terrain improvement. It's something I've been working on, tricky to balance as you don't want to obsolete all terraforming either

[Alpha Centauri Bear]

Fungus already had decent nutrient and energy output. I guess with that bases will at least be able to feed population and maintain facilities. Units can be impacted, though. But there should be trade-off somewhere.