I'm worried that all these new teleporting techniques and the ability to use a unit as a pylon may make the game un-balanced in the protoss's favor.
I always enjoyed seeing a huge line of cannons as my enemy coward to build a huge defense, only to realize he built only a couple of pylons which were easily taken out.
Then again I could be wrong, but another annoyance is I have to re-tune my micro and macro skillz all ova' again.
But the graphics! Still a toss-up on that one, I like StarCrafts 2D isometric view, and playing in 3D will seem strange as well, And I have noticed another thing the zealots voice doesn't seem to have changed much, and it still has the same chants and sayings as in StarCraft 1, and the "Nuclear launch detected" sounds exactly like in StarCraft 1.
Just some minor annoyances. (I'm a big fan, of StarCraft, and I don't like my child being altered in ways I don't like )