As for the crew size hindering boarding parties, yeah, that could be a problem, although I haven't seen any AIs build baseships. And I'm sure not gonna research them on my own
I've has trouble capturing colony ships & BCs, since I was only putting a single BP1 on each of my LCs, and two crew quaters fended off my boarding attempts. I ended up just shooting the BC until one of the CQs got blown up, and captured him with my third ship.
It would be nice if, when you used boarding parties, you could destroy some of the defending components before you died. Then, a series of capture attempts could eventually succeed.
As for trying to capture a baseship, I'd send a big fleet of captured LCs, which would run up and start pounding away with Large Antiproton Beams, or whatever my best tech was. With more than three times the tonnage in ships, I would expect to drop the baseships shields before taking 50% losses, and now short bursts of fire from each ship until there is only one Crewquarter left & no SDD. Then I can capture with a standard LC. If I was planning this operation for some time, I would also have a CR full of boarding parties (10 or so), and may have researched higher capture tech. Then I wouldn't have to do as much internal damage (only take out the SDD) to capture it.
The first capture always has to be analysed, the second one would be retrofitted to be, probably a support ship (repair/resupply and maybe a bunch of BPs for taking over the next Baseship)
Of course, if the AI dosen't build any baseships, the universe will never see one.