The key difference being they knew Bledsoe wasn't all that good, whereas I think they have a much higher opinion of Jimmy.
I think that's overstating things a good bit, though a few things are reasonable to note:
1. Pats had questions about Bledsoe
2. We have almost no idea what their true assessment of Jimmy G is right now (I think they like him--but they also did invest a lot more draft capital last year...for which there are good reasons)
3. Bledsoe was much later in his career than Jimmy G at time of trade (so, potential 'risk' probably is higher with Jimmy G)
4. Bledsoe had more years of control (though given his contract size and likelihood Jimmy G would be open to extension this is sort of a marginal thing)
5. Bledsoe was a sure upgrade for Bills, and while I think Jimmy G very very likely would be for Jets the certainty is still lower. We don't know that Jimmy G is a legit NFL QB, while we knew Bledsoe was (even if an imperfect one)
Bottom line, for me, is that Pats likely prefer not to deal in-division (and reports suggest that was the case with Bledsoe too) but ultimately will take the best return. They are not as adherent to received football wisdom as most teams...