I think the joke here is, in the first game with Altair (seen inside the water) you automatically die when you jump into water, while in the new game with Ezio, you're able to swim. I guess Ezio is mocking him?
Supposedly there's a line in there where Desmond says they've finally "fixed the swimming glitch." I didn't hear it myself, but I could have missed it.
I've played the game multiple times, but I never heard it. I would've noticed, and lol'd, if I had heard that. Many, many times did I accidentally jump in the water like a moron as Altair. I guess its understandable that a guy in the Middle-East can't swim though. Deserts, ect.
Its actually said in the manual that not swimming was a glitch in the Animus 1.0 (Assassin's Creed one), but they fixed it in the Animus 2.0 (important if you want to go around Venice).