I'm an experimental guy, not a numerical one, so take my advice with a grain of salt. As far as I know, fluent has advantages when it comes to parallel processing. And fidap generally does a better job with mesh flexibility. If I remember right, one is pressure-based and the other is density-based, although I can't remember which is which. I'd call tech support and simply ask them which is better for your application (the same company makes both).
Haf