Yeah I agree with your sentiments over the dex hahah. Hmm, I was thinking that the mass capture was that perhaps they tried to take over openly in the past and failed, though some of your ideas might work better. And yeah, the idea that trainers are to blame is a good angle I think.
Anyway, I was thinking about Team Phantom a little more and I guess that by making Pokemon very scarce, their value increases, so perhaps they rely on selling Pokemon illegally like you suggested? This is especially a contrary force working against the likes of obtaining a license and using dodgy Pokeballs, though I don't think they'd be supplying the latter to the public, rather creating them to be able to catch Pokemon without a license, whether it be illegally supplying people with the opportunity or doing it themselves. Maybe these Pokeballs have unwanted side-effects on Pokemon - e.g. more aggressive behaviour? I dunno.
Anyway, sharing a doc here, although I just keep a word doc with everything on my laptop.