There's been quite a lot of speculation based on that quote which really doesn't sound like it was transcribed entirely accurately, but that's neither here not there that Whedon is holding back Thanos until The Avengers 3, because that's somehow the big finale of the Marvel cinematic universe.
Honestly, that doesn't seem like even remotely the most plausible interpretation; more likely, Whedon is suggesting that the Avengers won't take on Thanos directly until the final act of The Avengers 2, and in the rest of the movie they will fight his underlings, because Thanos is just too powerful for them to fight throughout the movie. So, unless we get some major clarification on this quote, I'd say this is just minor plot information about how Thanos and the supporting bad guys will fit into The Avengers 2, rather than news about The Avengers 3, which I'm not even entirely sure Whedon is signed on to work on at this point.