I tend to only train them at the start to get the guilds. Once they are upgraded it seems to help get over the early hurdles. Merchants in particular without any starting bonuses just seem to get hoovered up by some 6-7 finance bloke camping around your cities.

I've had some success with assassins in my current Venetian campaign, getting the guild HQ up in Florence and killing off quie a few generals, including the Holy Roman Emperor twice. I'm not sure it makes that much difference to my campaign though, other factions seem to have no trouble replacing their generals. Has anyone ever managed to remove a faction through assasination? You'd think it's be possible when someone is down to their last province (although pointless by then of course). I slightly suspect the AI would just cheat and sprout new family members as needed.

It is very satisfying being able to deal instantly with foreign diplomats and princess who try for those persistent ( and often completely nonsensical) bribe attempts though.