I'm almost always renegade, so I always pick the renegade option. When my dad was playing Mass Effect I just started saying "DOWN!" to stop him from picking the pus... I mean paragon options. In real life I'm much nicer
I'd have definitely kept the base, but NOT given it to Cerberus. Or if for some dumb reason that wasn't an option, when TIM (not if, when. He's only missing an evil mustache) decides to be an evil git and go power crazy I'd storm his base and kick hiss ass. He should have known better than to resurrect a super soldier and give him a super team, then turn around and be an idiot.
Samara/Morinth wouldn't even be a question. It's just space paladin or space succubus.
I would have kept the data on the genophage, not for any moral reason. Why just throw it all away when some use could come out of it, use it to see the most vulnerable points of the genophage.
I guess the council would be the hardest decision for me. If I didn't already know the outcome would be the same, I don't think I would waste resources saving three people and a shiny ship when a reaper is RIGHT THERE.