I'm personally a fan of renovating like you clean, top down. All the movement you're gonna do is gonna affect your floors for the rest of the work... Especially if you're finishing any hardwood. Waiting for it to dry is a bitch. Especially if you need to move appliances or something.
At least that way if you spill paint or drop a door or a nail gun, you're not freaking out about damaging the nice new floors you just installed.
That said, I did install my baseboards after the floor last time I did it because I wanted to get as close as possible to my new floor and not use quarter round as a cheat.