Thunderbolt is actually based on the Mini DisplayPort specification. If anything, Apple will add this to the iPad, but it will look quite different than USB.
The next iPad, rumored for September of this year, is more likely to include major new features, including a higher-resolution display and more connectivity (i.e. Thunderbolt).
It's doubtful that the iPad is going to refresh that dramatically by September. It's even more doubtful that Thunderbolt would be in such a refresh – they would have to add PCIe support to their ARM SOC and that doesn't seem trivial.
(Though it's entirely possible it's in the new A5 and they said nothing about it)
I think Apple went out of their way to make it seem like iPad2 is a long-running product:
- end of video, Ive saying "iPad2 will define the category for years to come"
- 2011: the year of iPad2
Both of these are, I believe, explicit attempts to make people NOT think a new iPad3 is coming soon (so people won't wait, and will buy now instead), but in reality these two things perhaps support the iPad3 in September rumors...
Doesn't seem unreasonable coming from the company that claims to have popularized USB:
http://www.apple.com/thunderbolt/