Air to air is easier to make efficient and usually way cheaper. You can get a lot of bang for your buck with a front mount air/air setup and there's no maintanance and nothing to fail really. You add more weight, complexity, and cost with an air/water setup, and there are more things to fail. That's not to say there aren't some good reasons to have an air/water setup, but for street cars it's a hard thing to justify. You have to have a radiator, charge cooler, header tank, pump, coolant lines, charge tubing, etc. instead of just the intercooler and charge piping for something like a front mount air/air.
It really depends on the setup and the car, but I'd find it hard to lean on the side of the air/water for most situations. It's just really hard to beat an air/air for efficiency most of the time..
That being said, I'm going to replace my top mount WRX intercooler with a air/water unit this summer if I can scrape the money together. Why? I like to fabricate stuff.. If I were sane I'd just buy a bigger top mount or front mount like the rest of the world.

So to answer your question, my opinion would be a bigger air to air setup..