I'll go ahead and answer my own question a bit too.
But firstly, yeah, I don't like the whole factions idea. While it is IC, it doesn't offer much player-control, which is part of what makes Yliakum great.
The main thing I have with having alts in guilds is the concept of alts in the first place (which is for me, a bit of the pot calling the kettle black. I have been renowned for having several alts before >.>) but having had several alts, I also know that I don't play them all very regularly. I think the best players in PlaneShift are able to devote their time to one or two characters, and have a few bit players. To be a good roleplayer that contributes to a guild, I think you have to be more than a bit player: you need to be a fully fleshed character.
Not only do alts kill guilds, but they can degrade the game, too. If players get attached to your alts and you don't have the time to play them, you're putting people off and killing 'threads' of RP. Why? Because people get disinterested and move on when you can't dedicate time to involving them or being involved with them.
Idk. I've tried to get it down to where I play one character constantly (or have been, with Wulfar - I think it's getting time for him to move on and I'll play someone else), and maybe one-two alts (Lyla atm), with a few bit characters that I can bring on for an as-needed-only basis. That way, whoever gets a hold of me, be it for a guild or just general RP can have my undivided attention.
There are people who multitask better than others, granted. But I find that if you spend so much time bouncing ideas into alts, you lose a lot of what makes having a main special: truly fleshing it out, truly making it special, and truly being involved on a much more than superficial level with PlaneShift and its players.