Takedowns are weighted way to heavily in the judges' eyes.
Elbows on the ground take away from the submission game.
Pressing an opponent against the cage counts as cage control even if the person pressing gets elbowed upside the head repeatedly.
Short rounds match the pacing of a wrestling match and don't let submission grapplers work effectively, making them throw up low percentage submission attempts too often.
Refs are too quick to stand up fighters after a takedown if the person getting the takedown ends up in guard and doesn't try to advance, even if the person on his back is mounting an offensive and working for a submission.
Basically, wrestling is a great way to control your opponent, but not attack your opponent, yet judges look at wrestling advantages and weigh them way to heavily compared to other attacks. How many guys have won rounds they've been grossly outstruck in because they landed a double-leg takedown off the cage, even though the guy they took down got right back up?
Watch GSP, Rashad Evans, John Fitch, Gray Maynard, Sean Sherk, Ryan Bader, Matt Hughes, or early Josh Koschek for what I'm talking about.
Especially the Hughes vs. Serra fight. Hughes got takedowns often, but Serra was attacking off his back when he was down and actually got closer to winning the fight than Hughes did.
Or any of the fighters out of Greg Jackson's camp.