I see the advent as more evil than the TEC in the game due to the fact that their weapons are things that torture the mind.
How so? Off the top of my head, most of the weapons just suggest that they are strengthened through psi powers (extra focus on a laser, special accuracy, telekinetically reinforced hulls) rather than attacking the enemies brains directly.
The only "evil" stuff I can really think of is their penchant for a form of mind-control, (their culture mechanism, some capital ship powers) not very nice, but neither are the "traditional" means of takeover. Heck, the TEC seems to specialise in using long-term radiation warheads on planets, (and ships IIRC) not exactly sweetness and light there.
In my opinion, they're just at war and using all the resources they have available. You use the stuff you're best at and, lets face it, the in-game representations of the Advent (faces, the loading screen lady) don't exactly suggest much in the way of brute physical strength. You could even argue that since the Advent focus on converting the enemy to their cause rather than annihilating/enslaving them they're taking the humanitarian option in a brutal war of conquest.
If you just disregard the lies of the TEC propaganda, you'll soon realise that we offer a better way of life and that our sole purpose is to Unify everione in peaceful harmony. [telepathy]Come join us, come with us, come join us.[/telepathy]