I personally nearly always end up with all of the colony management skills. Like 90% of my games i skill them, because boosting passive income is my idea of fun. It also is my personal main endgame goal. Get as many Colonies as possible and make them self sufficient militarily and profitable.
These skills are definitely not boring at all. Sad to see them go away.
I think the main issue with colony skills isn't that they're not good, it's that they're mostly replaceable by Alpha Cores. Once you're able to fight [REDACTED] fleets, Alpha Cores are essentially unlimited (just based on how much time you're willing to spend farming them), whereas skills are limited to 15 total. So in that situation, it's better to just use Alpha Cores as colony admins so you can maximize your skills.
Or Colony Items, which are much more interesting and have more levers to pull than Skills. Ultimately, all colony skills boil down to generating income and keeping that income safe. I agree with Alex in that printing money can be handled outside of the Skill system. The only Skill that might still be necessary is something to improve the number/efficiency of Admins but even then it should probably be tied to some other campaign layer.
Colony items are not that interesting when they spike Pather interest. I avoid Hypershunt Tap like the plague because I never ever want cells on my colonies, not after the painful experience of 0.9a. Two colonies are locked with pristine nanoforge and synchrotron because I need them to meet demand for Military Base/High Command. That leaves two other planets with one colony item each. Ideally, they should have Dealmaker Holosuite (or maybe Biofactory for the Light Industry drug planet if core worlds were not wiped out).
Industrial Planning feels like a tax because it seems like demand always assumes admin has IP, not to mention that meeting 9 or 10 demand for the lamp or tap assumes player min-maxed demand stats.
It would be nice if player could rule more than four planets without using cores. Even if getting colony skills was sub-optimal (thanks 0.9.1a Pather bug), at least it was a way to get a kingdom as big as the Hegemony or League.
P.S. Four planets feels kind of constraining when I need two systems with two planets or one system with four planets because of required colony defenses to avoid babysitting.
I think the primary reason that Alex is dropping a player's access to colony skills is that making them available basically forces a player to choose between either "route" (for lack of a better term), but choosing colony skills over combat skills means that a player will conversely have that much harder of a time beating the story line, unless they respec (since player doesn't yet have option to drag a second fleet around with them). So the least complicated solution is to remove option for the choice entirely (and either "fix" and add back later, or just move on).
Still, I'm of the opinion that the colony skills should be kept for colony admins, and player at most might have to choose a skill that allows for either handling more admins, or just reduces the penalty for having non-admin colonies (so only your best colonies need/have admins, in the event you don't want to use alpha cores). However, the second half of this could admittedly be achieved by just adding more unique colony items that player can find, which would sync in nicely with the possible change to tech mining (where it would generate quests for unique colony items instead of just dumping out items randomly). Plus, I'm sure at some point there will be another event chain building on a player's alpha cores going rogue (which happens when player sometimes tries to remove an alpha core from being an admin). Which would be cool for player to basically run into the same issue that TT had 200+ years ago... which can be avoided by using normal admins, but tradeoff is that player's faction is limited in how far it can grow.
Edit: spelling, grammar, yo mama...