I know this thread is old, but thought I'd throw in a few words. I have had only slide ins, but I hang out at the shop quite a bit and have asked many guys about the pto's. Hydramaster has the best pto, and every guy I have asked, including the mechanics, agree. I wouldn't buy anything else from them, the slide in units from them are total crap. For some reason they really got the pto right. I have a Hydra master 427 slide in, less than two years old. That thing has been to the shop WAY more than my 4000 hour prochem EVER was. And I'm not the only one. I have rarely heard of any problems with thier pto's.
As for the differences, the pto's are much simpler in design and take less to maintain. They do take a toll on the van, burning up seals and motor mounts, especially here in Arizona. Maintenance on the van must be kept up to par. A slide in will require more maintenance, take up more room, but may be hotter and easier/cheaper to fix if there is a problem. You can fix it yourself in some cases, while a pto will more often require a trip to the shop. And of course, the pto goes with the van, so taking it out requires a little work and getting everything back to stock if you do so. A slide in requires a forklift, that's about it.
I am currently working on building my own slide in out of an old frame, tired of having to fix (spend money) on this stupid 427. It's a lemon, so I'm going back to my roots so to speak and making a machine that is simple and easy to fix. That's what's important over everything, that it does the job, is easy to use, easy to maintain and most importantly MAKES money, not TAKES money.