His TT wasn't that bad, he lost a little over 2 minuten on Schleck, and a little under 3 minutes on Contador in a 50km TT. I really don't see him losing much less time in a TT in the future (maybe a minute faster, losing 1 minute to Schleck and 2 minutes to Contador would be a really good result for him). He lost quite some time on the cobbles yeah, that was a one-time thing, although I do see him losing some time to Schleck in the TTT this year.
Overall, he lost the most on the climbs. Schleck and Contador were clearly on another level on the Madeleine and Tourmalet. If Gesink wants to win, he doesn't just have to match them in the mountains (that would be hard enough), he has to gain 2-3 minutes in the mountains, to be safe for the time trials. He probably has to improve a couple of minutes (compared to his 2010 form) on every mountain top finish, I just don't see that happening in one year.
I don't understand were your Leipheimer comparison comes from. 2008 was Leipheimers last great GC, the guy was ancient already, after that he got worse, and Gesink got better. Contador and Schleck are in their prime, they're not going to get worse for a long time, Schleck could probably still improve. If Gesink wants to bridge the gap, he has to improve, he can't count on the competition getting worse (what happened with Leip).