It has been countered, many times. (Prime example is with Kabuto in part 1.) That's why he made "Odama Rasengan" and "Cho Odama Rasengan" and etc. Also, the reason he hasn't gotten countered that much from sage mode and on (even if it's hard to tell in the manga) is because he's moving at the speed of light.
I think the teleportation, alternate dimension, and worm whole stuff is fine. But I guess that's just preference. Oh, and he couldn't make Tobi's leg or phasing disappear because: A. Tobi's is more powerful. and B. He just figured out now that they're the same. Also, he gets hit now because Kakashi just figured it out. :S
I think he just sat there because he wanted to see what they would do. He's probably a cocky mother fucker that is so arrogant he thinks he can't lose. This happens all the time in shonens. (Look at Vageta in DBZ, he did this like 50 fucking times.)