I've been kayak fishing for a few years. I've never tried the sit-on kayaks, preferring and owning several sit-in kayaks. My wife picked up a Perception America kayak, (15.5 feet?) for about $550. It works great for fishing. I prefer hers for fishing for 1 particular reason: the length. I can't fit fishing poles into mine quite as easily. I've never bothered outfitting mine with any special equipment to make it easier. i.e. rod holders or anything.
Oh, and in my opinion, kayaks hold their value fairly well if you take care of them; at least in my area. Of course, it's easy to pay too much in the first place, in which case they of course don't hold their resale value.
Also, yes, you can certainly "sneak up" on fish - a lot of fish are spooked more easily by larger boats.