*This is a very polarized topic, so I'd request that people don't flame and/or go too far off track. This has been covered in the past, so this thread won't re-invent the wheel. Let's see how it goes.....*
Professional schools are free standing (not associated with a university), and were basically a response to produce more trained (doctoral) clinicians. Some argue they are not needed...I happen to think they have a place, but I think they need to be overhauled, downsized, and the quality made more consistent. (obviously, just my personal opinion)
I think the training can vary greatly; I know graduates from some that are excellent, but others who suck (to be blunt). Traditional programs can also produce excellent/poor clinicians....so YMMV.
They tend to not be very well funded (if at all). I think this is one of the biggest knocks. The rep of the schools definitely vary......the funding and larger size tend to be the two biggest knocks. I think you can still get very good training, but it will be more costly (obviously) and you need to make sure to align yourself with the right mentors. Traditional programs don't guarantee great (or even good) training, so make sure to do your homework.
Basically......do your homework, whether or not you are looking at traditional programs or at a professional program.
-t