Trying to counter Velasquez' take down attempts would have made Dos Santos more prone to the take downs. He may have tried with the more lack luster TD attempts, but Dos Santos is not really a kickboxer. Unfortunately he had nothing offensewise than his boxing and Velasquez successfully canceled that.
It does make him more prone to takedowns but he does have to do something to take the initiative instead of being constantly on the defensive against Cain. JDS isn't really a kickboxer as you said but he better learn fast since his height makes it harder for him to catch someone with punches when they're going for a takedown.
The other option I can think of is better use of angles and staying the hell off the fence like his life depended on it. There were too many times when JDS backed straight away from a takedown or put himself into the fence where he got clinched and beaten on. He needs to slip to the side more and use the angle to hit Cain with punches, then keep circling out to try & keep the distance open. As soon as Cain starts to shoot in, sidestep and unload a couple quick hooks to the body.
And the more I think about it, the more it puzzles me that JDS didn't throw knees when he had Cain in the neck clinch. He blasted Roy Nelson with a bunch of knees from that position so it's not like he doesn't know how to do it. As you said, when you have the shorter guy in the clinch like that you should be working him with knees. He did that with Roy then mixed it up with punches, I just can't figure out why he didn't do the same to Cain.