1. lack of consistency
2. lack of optimal movement
3. lack of a more dominating serve
he can compensate for some of his deficiencies if he can develop a far more dominating serve. that goes a long way.
top players move better and they are simply more consistent. he is also terrified of the net. no harm in going forward and giving them different looks. you should be able to go in when you get or create those opportunities.
Now this is a rare sight. A pretty much perfect answer right off the bat.
Maybe toss in "mental strength". He doesn't quite seem to believe that he "should" be winning the big matches against the big boys. Unlike the big boys that just simply believe they should win pretty much all the time.
Berdych can also have surprising losses against lower ranked players. Something that you rarely if ever see from the top 3 (and even the top 4, except when Murray is sulking, which hopefully won't happen anymore).