Leadership 4 is the big one. No way to get Ground Operations without locking the player into Leadership.
This is why I take Automated Ships, even though I much prefer Special Modifications. Spec. Mods make some flagships noticeably better, not to mention the rest of the fleet to a lesser extent. (That said, watching Radiant slaughter things is fun.)
The only reason to remove Spec Mods is envy (from those who take Auto Ships just to avoid locking skills for full respec).
Officer management is an easy talent to unlearn, 0.9 already had a setup for going over officer cap. You lose the ability to assign 2 officers, so just don't let the player assign them. EZPZ. The two last officers might be unequipped "at random" or maybe all officers get unequipped for the player to deal with. Unlearning talents is a rare event so that's not too inconvenient.
Yes. Why can player unlearn Colony Management (same deal, but with colonies instead of officers), but not this?
If player did not want to use cores, but wanted Industrial Planning to meet demands, he can game the system by getting Colony Management first, install admins, unlearn it, then get Industrial Planning for five worlds with IP. Third admin cannot be moved, but is not removed; kind of like a sticky Alpha.
Officer training is the HARD one. Officers are allowed a bonus level, with associated +1 skill and +1 elite skill. If the player unlearns the talent, what to do? Do officers suddenly lose their levels and have to be reset? That'd be annoying. Do officers start getting "unruly" that their skills are too good for the player? Will the player have to delete all their elite officers and start from scratch? That'd be a huge setback and way worse than the simple loss of talent. It may be better to remove officer training entirely.
The idea may simple enough. All level 6 officers lose a level and a skill is removed. Maybe not be the one the player wants, but too bad. However, that might hurt level 6 and 7 officers found from derelicts.
As for replacement for higher level, maybe give officers some buff like more damage or ECM. It is not like player will install them on a tanker or passenger liner.