Traditionally, I've used the regular trooper the most, by far. He's versatile and powerful. The rifle works good in close combat but I can snipe as well. (I snipe way better with the trooper than the sniper. And the elite sniper rifle sucks). The elite rifle is awesome.
But recently (last time I played) I started using the Engineer, and I was extremely impressed. Detpacks can be fun. The health and ammo thing is fricking awesome. And the Shotgun is actually really good, a lot better than I thought.
So I've started to use the engineer more often. But I think the regular trooper is still my favorite. It's tough to say though.
Least favorite unit- Dark Trooper. Try as I might, I can't ever like the Dark Trooper, in either game.
As for Heros, Han Solo is awesome. He basically has an elite rifle with unlimited ammo, and hero health. Plus, he's Han Solo. Boba Fett is cool too, but his limited ammo gets annoying, moreso than it is for regular units (due to longevity and the fact that death doesn't work as a convenient reload).
God is a placebo with nasty side effects.