Rocket's got the best motivations, they just want to run a business, though they come off as pathetic in Johto. Pretty bland admins in Johto too, though I blame the stifled script of English HGSS.
Magma and Aqua are absolute dogshit in RSE with bland admins and absolutely zero thought or caution placed in their retarded plans, ORAS fixes all that but they still at the core have retarded motivations and the whole "Zinnia is the brains behind the Groudon/Kyogre incident" thing undermines them.
Galactic is solid, memorable admins, encounters almost all play into a bigger story, grand but not totally retarded motivation. Pluto totally sucks though and felt out of place. Not much else to say about them.
Was never a fan of Plasma, but it's mostly a form of bias because I get too pissed over how the first encounter is vauge as to whether they're well-intentioned or not, but then they are shown literally kicking a Munna and it seems clear they're just plain bad, then they barely try to do damage control afterwards until they make the faction split clear at the very end, which is the only point that the dialogue does a good job of making it seem like any grunts care about liberating Pokemon. BW2 terrorist Plasma is bland I feel, but seeing the clash between factions and Ghetsis trying to kill you was cool, and your rival's direct involvement with the evil team through the events of BW1 was nice.
Flare I think is generally pretty underrated, the grunts had very amusing dialogue to me, they were like Galactic in that most of their encounters played into their grand plan, and I like Lysandre, Xerosic, and Malva a lot. I like the general background to the team too, but the issue is while there's a lot just told to you or that can be inferred if you think enough about it, none of it is really shown or elaborated on. Like several things in XY. Also, the four scientist ladies are completely forgettable, easily the worst admins. No decent fights either.