So first off, what new players will have to realise quite soon, is that right off the bat you can only have a very limited number of colonies without penalties (2 governed by the player and 2 more governed by admins).
I'll point out in 0.95.1a the administrator limit was raised to 3 for everyone and the player running planets is a soft cap. The stability penalty for going above the soft cap for the player is potentially a non-issue for small numbers of planets given you can reach +14 to +15 stability on a fully built planet (and go as high as +17 if you spend story points in a system with a domain comm relay).
So you can run 3 planets with a -2 stability penalty yourself, 4 at -4, and 5 at -6. That level of penalty is not too much of a problem on fully built up planets. I wouldn't want to add free port + commerce to those worlds, but you've still got those 3 admins to run those kinds of worlds (which typically tend to be profitable enough that even a 20k salary admin is worth it on a size 6). Overall, a no AI core player can hit about 8 worlds with 8 or higher stability, which strikes me a lot of worlds. The fact that you can spend credits to reduce some stability penalties makes raids and pather events relatively painless to handle, even with a baseline of 8 stability.
The other thing one can't help but realise is that there is only 1 skill affecting colonies currently the player or admins (in which case it's a watered down version) may get: +1 stuff produced and 50% more Heavy Industry ship production value. Starting out, choices here are hard. For the player, the skill competes with practically every other one, and as it does not affect your fleet in any direct way, it is easy to pass on it.
Since Industrial Planning is tier 3 in Industry, if you're going for Industry 5 for fleet purposes (Hull Restoration and Derelict Operations both can be fairly significant fleet boosts), the opportunity cost doesn't feel that high to me. Your 4th industry pick is always going to have to be a non-combat choice anyways. If you're going only for the colony skill, so going 3 deep in Industry, then I agree it's probably a bit too costly for most fleet focused players.
Now to contrast it with how it used to be, admins used to be able to get 2 skills (out of 3) at max and had lower costs in comparison. The skills were +2 stability bonus, +1 industry production and +20% accessibility bonus (although I am not entirely certain about the third one anymore). You could boost accessibility for farspace colonies, boost stability during a raid or otherwise mix and match admins to maximise profit. This versatility is currently missing.
All that versatility boils down to is more or less credits at the end of the month. It doesn't really change how you play the game. If you colonized multiple planets in a system, multiple military bases means the defensive portion of stability doesn't matter that much. So that means when I'm comparing stability, industry production and accessibility I'm just looking at one number going up and down. I didn't find it all that engaging. Are you making more credits at the end of month with Admin 1 instead of Admin 2? Yes or No. If I'm having stability problems due to recent unrest, I spend credits on the stabilize button. I'm not trading off current production versus future research for example, like I might do in a 4X game.
And now for the meat of the matter: the glowing blue balls, aka Alpha Cores. There are some slight differences between them and administrators. First off, they can command ships. Which is neat. Second, they get the industry skill, without billing you 20k per month. You can also assign them to industries and structures for various kickass effects and so on and so forth. The Hegemony gets a bit *** and the pathers will not stop hassling you, but hey, you were going to have trouble from them in the long term anyway. On, and there is another great characteristic they have. You can have a bazillion of them and and colonise the entire Sector if you so wish.
As long as the colony stays at size 3, the Hegemony and Pathers won't hassle you at all, nor will any major faction. So size 3 alpha core waystation only colonies aren't really attacked by anything (except maybe pirates occasionally?)
I personally think the biggest difference between admins, the player, and alpha cores is the fact you have to fight space ship battles to get significant numbers of alpha cores. You might get 1 from a particular bar mission, and find 1 or 2 during the course of exploration, but the general method of obtaining them is fighting Ordo fleets. You essentially need to have already beaten the game and put red beacon systems on farm in order to get significant numbers of them. Unlike admins, which involves mostly waiting and flying between planets and hoping for the RNG to roll well that month, and can be gotten at any stage of the game. Given fighting fleets is what the game is primarily about, the campaign giving you a reason (better colonies) to do so against hard enemies makes sense to me. Although late game colonies with investment can still produce plenty of credits even without cores.
So considering the above, if the player forced, or at least coerced into using AI Cores in the long run? Sure, initially it is beneficial to only have colonies using admins, so that you don't *** off the Hegemony before you can handle them, but still, if you want to roleplay as an honest to Ludd pather, you cannot claim all habitable worlds in the name of Ludd without AI interference (or editing the settings file for a more reasonable admin number like 200 or so). While combat is undoubtedly the focus of the game, are there others also a bit bugged by this? I know, it's not a 4X game, still, small size 3 outpost colonies at strategic locations should not be too much to ask for, are they?
Well, you're only forced into if you want more planets than you really need to "win" the game. At the point you are pulling in more credits than you can possibly spend on your fleet, is the point at which the game is giving you no incentive to create more colonies. I'll also point out that in vanilla that there's only so much industry profit to be made. Player planets don't add to demand, and thus don't increase the global market value of commodities. Creating more planets with industries reduces the profitability of already existing planets. So you're basically limited to population and infrastructure income scaling once you've saturated the markets.
So colonizing all habitable worlds in the sector, or trying to have 100 colonies are mostly self imposed challenges, rather than something necessary due to gameplay. Nothing wrong with wanting to play that way. It just doesn't bother me that this isn't well supported without alpha cores. The tools available (admins and player skill) are sufficient to reach an end game passive profitability state even without cores, which is all that I'd expect out of the game. The fact that there's an end game fighting option for those interested in those kinds of challenges, but doesn't really impact the early and mid game balance also seems fine to me.
Actually, does the game engine handle that many player colonies well? I could imagine the campaign layer having significant slowdown or memory issues with 100 additional colonies, but never having done it, don't actually know. I do run into some memory issues if I crank Nexerelin faction starting worlds up high.