No. It really wasn't. The Jets STILL don't have any money. The agreement with Fitzpatrick puts them like $7 Million over the cap. They're going to have to make some pretty serious adjustments to fit him in. (or, according to Over the Cap, use some sort of "voidable contract structure", which I don't really understand) And when the "The Jets don't have the money" talk was going, Wilkerson was counting a whopping $17 Million against the cap (Now $10 Mil after signing his extension) under the assumption that he'd be playing under the franchise tag.
Back in May/June when the whole "Fitzpatrick will play for $12 Mil" talk was going on, it was basically impossible for the Jets to sign that deal. The last minute deal with Wilkerson opened the door a crack. The Jets 3 year discount offer to Fitzpatrick wasn't really about getting him for backup money in years 2 and 3, it was about creating a contract structure that would keep his cap number for this year as low as possible (Giving him a low base for 2016 and spreading out a signing bonus over 3 years) and minimizing the financial impact if they chose to cut him after this season. It was the only realistic way they could fit him into the salary structure (other than him taking the $8 Mil for 1, which was never going to happen) if Wilkerson didn't re-up.
This really isn't that difficult to understand. The Jets wanted Fitz (and needed him to challenge for a playoff spot. As I've said, I don't think that's happening anyway) and Fitz knew he had exactly ZERO other suitors. Throughout this entire process, the Jets' stance has been about the realities of the salary cap and the structure of their team. Fitzpatrick's stance has been about his own pride (hard to justify taking that much less than guys like Osweiller and Bradford after a career year) and the totally reasonable desire to set him and his family up financially going forward.
So did Fitz "win" here? I guess maybe he did. He obviously had the support of the locker room and he got a nearly 400% salary bump off last year. But as far as negotiation "losses" go, this is a pretty good one for the Jets. They've put together the best team they could for this year, and their cap hit for the QB position is one of the lowest in the league (excluding guys on rookie contracts). This is a zero risk deal, as they were gonna have to spend the money anyway. The only people who lose here are Geno (who will still make the team) and whoever has to take a pay cut to fit Fitz under the cap.
The only potential downside here is if they decide not to carry 4 QB's, can't sneak Petty onto the practice squad and he somehow becomes something down the road.