You know, i like pocket holes. I think that theyre a pretty neat solution to a problem, the jigs are an elegant sort of simplicity, and for certain tasks theyre by far the fastest way to get something done.
That said, pocket screws are a horrible method of joinery.
Pocket screws are made for cabinetry. If you need to make up a carcass, then a Kreg jig is going to be the fastest strong way to get all the sides together. The screws will hold way better than a brad nail or similar, and dont take nearly as long as a dowel. For joinery though, theyre crap, and i dont care what the manufacturers say. The problem is the joinery is completely dependent on screws. Screws dont hold well in wood. Over time, wood compresses around the screws, and the holding power vanishes. No holding power, no joint, period. If you try to use a pocket screw to secure something like a chair back, every time you put any sort of stress on that back youre going to be compressing the wood around the screw and gradually working it free, and that joint will fail very rapidly.
In the design of your desk, pocket screws are a notably horrible method. See, the problem is is with a table like that, if you happen to bump into the side of the desk youre going to be putting a huge amount of racking force on the joints, and that will rip the screws free in no time at all. Doesnt matter how many screws you put in the joint, they arent going to hold.
Now, there is one benefit to pocket screws in joints like that; they make fantastic clamps to hold the pieces together while the glue dries on an actual joinery method. In the case of your design, adding some dowels in the joint to actually take the load, then using the screws solely to keep things held together while the glue on the dowels dries, will result in a much more sturdy design. Still though, not a bad idea to add some gussets to those corners. Bit of reinforcement never hurts