From what I have read, certain individuals such as Orton and some other main eventers all put the boot in on Kennedy, and said he was a liability, and was constantly putting others at risk as well as being injury prone.
Kennedy has made a statement about this, that while somewhat over the top, and not pointing any specific fingers, he said something like "If I chopped your legs off with a samurai sword, and didnt tell anyone it was me, would that make you accident prone?"
Batista though suffers from that age old problem that overly muscled up guys suffer from, and is easily injured.
It probably doesnt help him that he is in his 40s as well, and is a highly likely case for potential steroid use in the past (or now, depending on how you look at it).
As you say, Batistas size probably helps him, but I also think that as a main eventer, and someone who apparently has some friends higher up the ranks, he gets more leeway than others.
Kennedy was a far better worker, better on the mic, and a kiss up, but none of this matters if you have enemies with pull, and Vince doesnt particulary like you.
Kennedy has actually said he is friends with Batista, and has defended him, so its quite funny that the two are so comparable injury wise.
Also, Bobby Lashley has made comments that he feels Kennedy is not a particular liability in the ring, or works any stiffer than a lot of people (another thing thats been aimed at Kennedy).
