1) Heat dissipation - the stop heats up verrrry quickly if you ever use a rack you'll for sure note the difference, a rack is much better equipped for this so you don't glaze or burn through your rope (or your hand!) due to the surface area - there is much more material to absorb and dissipate the heat and the rope doesn't follow nearly as torturous of a path.
2) Really want to squeeze a handle that long?
Dang my hand hurts and cramps on 100ft/30m with a stop!
3) Variable friction control, depending as to the type of rope, dirt/moisture/etc all add weight and make the rappel tougher, you could be dealing with up to 10 pounds (4.5kg) of weight per 100ft/30m of rope. The difference in friction at the top vs bottom with such a change of weight, is huge. A rack is meant to handle these changes smoothly, effortlessly, and safely. You never need to feed rope, you never speed up too fast (assuming proper handling of the rack, but it is specifically designed for this!)
4) Eventually you get to the point where you can't even physically rig in a stop, or move at the top at all even if you get it rigged in, as the rope weight increases. I hear some folks with stops deal with this by using it in C configuration....now I guess I could be missing something here but that seems dang dangerous! We make long 24" specialty racks for long drops for a reason, it's the only way to get it rigged on, and moving, when you are dealing with that kind of weight like El Cap, a vertical half mile which gives about 200 pounds (90kg) weight to start with. Extreme example but gets you thinking.
If you are worried about "what if a rock falls and hits me and knocks me unconcious, a rack won't stop me like a stop!" we have solved this for long time, French Wrap (I think it perhaps has the name there of "Autobloc", a prussik loop wrapped around the rope typically 4 times spiraling upwards from a carabiner on the seat harness and then after the 4th complete spiral hooking back into the carabiner). In fact, on long rappels the rope weight is too much to physically manage a lock-off, and the FrenchWrap is how you stop to lock off!
For versatility, heat dissipation, ability to handle long drops up to a half vertical mile plus, racks win hands down.
If you want training in long single-pitch drops...welcome to come to TAG, we seemed to get Josh addicted while he was here, and our racks are wayyyy better than the short 5bar petzl ones. If you hate racks, and have only used those or similar, come here use a standard 14" with a hyperbar. Locking off and on-rope manovers are a breeze, and with training it will handle up to about 1000ft, although once you get up to 600+ feet jumping to an 18" frame makes your life easier (I prefer starting and staying on at least 5 bars, minimum to be safe is 4 bars).
A video I made of Whitesides last month (~700ft freehang rappel, training for Golondrinas which is over 1000ft!) shows my rack and French Wrap. When I'm stopped to video, I'm sitting on my French Wrap, the QAS is simply there as a backup safety since I'm just chilling hanging out.
VBATS Rappel at Whitesides, August 18, 2012
tl/dr: Long rope rappels are a totally different animal from all this alpine-style srt, requiring completely separate skillset and experience.