I think they do. They already started writing it a while ago.
Keep in mind that Spider-man 2 came out only two years after Spider-man, and people see that as the best movie. But they pretty much knew where they wanted to go with Spider-man 2 after Spider-man came out, namely Doc Ock since he was cut out of Spider-man, and they were able to start doing the train sequence really early into production.
Spider-man 3 came out three years after Spider-man 2. Definitely didn't rush it, and well . . . it's not always about length. Fox definitely mishandled X-men 3 for not locking up Singer and everyone asap after X-men 2.
They already have the cast, crew, and what not, and hopefully outside of Don Cheadle, there won't be too many other drastic changes. I think they could use a better music composer IMHO. Wouldn't mind a change in the music.
I mean the Rhodey thing is disappointing more than anything, but it could've been worse. Losing Favreau or Robert Downey Jr. would've been a lot worse.