The biggest issue is going to be that Alex wants colonies to be a tool for solving the endgame, but he is unwilling to say anything about it, so we just have to guess what he wants colonies to do, or basically what does the order tab do.
This is the question, basically. I think Alex was intending to have colony/colony skills basically complement the orders tab so that anyone who went colony instead of ship combat skills could deploy way more stuff from colony to make up for cruddy combat skills. But instead he just threw in the towel and added full respeccing for whatever reason. Not like slow partial respeccing (where player can only reskill like 1 skill per cycle after max level reached), just straight full respeccing. Definitely solved a lot of issues (and a lot of complaints), but hip shot solutions do tend grate on basically anyone who isn't positively affected (so both anyone neutral and those negatively affected). But now that respeccing is in the game, I don't expect it to get dropped when mythical colony update arrives.
As for OP about colony skills, IMHO only allowing admins to have colony skills seems most reasonable solution with least ridiculousness. Removing them from the player meta/skills next update might be a compromise, but definitely a compromise I could get behind so long as admins don't become generic stand-ins for misfires of colony game loop. Since otherwise basically forces player to use alpha core admins, which appears to be a trap for end-game: