I like them all, basically. What I really like is the organic architecture of the Ark, so any and all Ark maps are my favorite to play for aesthetic reasons. I can play with crates anytime.
Ark architecture, I can only get in Brink! 
I also have two points of criticism:
As has already been mentioned, the ease at which the Resistance can dominate the first section of Container City and thus fish-in-a-barrel the enemy as they come from spawn is unacceptable - at least, this is the case with Bots on Hard, it presents no challenge. The map should be tweaked with a third exit added, to allow people (bots) to get out of original spawn.
Second, any map (and there are several) where there is a lot of running which leads to “Corpse Bridging” as Tycho from Penny Arcade calls it, needs to be tweaked somehow. Remember the saying that “the farther you have to run, the quicker you die when you get there”. What can I say, Battlefield:BC2 spoiled me forever. Squad spawning is a revolutionary innovation, and while it may not suit Brink, something needs to be done about these distances.
I voted for Reactor because I win on that map whether I am playing as Resistance or Security (i.e., it seems balanced to me), and I like the first set of objectives the most.