Right, yeah - the Remnant ships are kind of OP for their size; not universally, but they generally are better in some aspect or break some general rule - such as, say, the Brilliant having access to ballistics where normal high-tech ships wouldn't to that degree. The Radiant is definitely where the gap really opens up.
If remnant ships are overpowered in player's hands (only true for exactly Radiant), why not just nerf them when recovered? Remove some weapon mounts, reduce skimmer to 2 charges and say those are lasting battle damage that can't be restored.
It actually does get nerfed a bit - due to how the skill works, you'd only be able to get it up to a bit over 40% CR when captained by an Alpha Core.
Not being able to pilot just feels really bad, especially since is has been waited for for such a long time. I want to DO cool things, not WATCH friendly AI do cool things, dammit .
Ah, on the one hand, I hear you! But design-wise, it's just exactly that - the skill you pick when you want to watch friendly AI do cool things. Loosely, it's sort of the same kind of appeal as a pet class in an MMO. Plus, there's the whole "set an AI core to pilot it and configure its skills" aspect. So you're still doing cool things, it's just in a different vein.
If you want to do cool things more directly, the other Tech 5 skill, or the Combat 5 skills, or, heck, a bunch of the other skills, too, have got you covered.
That said: I could totally see some kind of very-OP-expensive-and-with-downsides "Command Module" hullmod that could be installed to make an automated ship pilotable. Gets a bit weird with the "install hullmod, make into flagship, remove hullmod" sequence, though; so more in the "potential neat idea" category rather than anything that's planned.