I read that Malice + Brillance is a good combo. I can see why it would be, but brillance only does 250 dmg.... so even if I have everyone take 30% of that, it's not that great really. And Brillance only seems to hit 1 target, rather than a column, am I supposed to be trying to line up his ships and then fire?
Yes. The point is that Malice affects a group of ships, and so does Brilliance (Brilliance is 250/second for 7 or 8 seconds, actually). Thus, each ship that gets hit by Brillance that's also Maliced will spread the damage. Brilliance stops at the target you picked, and hits everything caught in the cone. So when you line your ships up you always want to pick the farthest target.
Anyways, another question I have is with the mothership, the resurrection ability, how does that work? I don't lose my caps much against the computer but on a big map I could see this being good, how does it work? Are all the crews I've ever had just out there in ghost land and if I cast resurrection on a low level ship, the best ghosts will hop aboard it?
Basically. Resurrection will make a lower level capital ship the same level as the highest level capital ship that you lost. So if you lost a level 10 capital, build a level 1, and use Resurrection on it - instant level 10

Oh yeah, and as much as I like Malice, what's the point in ever going above level 1? Normally when you hover over level 2 it shows you what gets improved... but with Malice, there seems to be no benifit in upgrading, so although it's my favorite ability, I don't bother to upgrade it.
Number of targets. The info card never shows targets affected, but it's 8/16/24 per Malice levels.