The ACF forum is a good place to ask strategy questions specific to your team.
As for the Jets defense, they have two big problems. One, they aren't really good at stopping the run. They have an undersized out-of-position and overrated DT in Dewayne Robertson whom they are lining up at NT. Shaun Ellis is an undersized 3-4 DE also (about 280 lbs), and Vilma is an undersized interior LB in a 304 (he's 230 lbs). All this has led to teams with good O-lines being able to maul the Jets with the run.
The second problem is very little pass-rush. The LBs aren't much for getting pressure on the QB either. I believe that the team leader in sacks is safety Kerry Rhodes.
What the Jets do have is a pretty good secondary. Andre Dyson has three picks to lead the team, and Justin Miller and Kerry Rhodes are also around the ball. If your league lumps special teams in with defense, the Jets are a mroe attractive option as well, thanks to the return abilities of Leon Washington, Justin Miller, and Tim Dwight.
I imagine that most teams think they will improve as the season progresses, and perhaps the fact that the Jets are learning a new system gives some credence for the belief that they will improve. Personally, I don't know.
I figure Mangini is not stupid. He knew that the Jets didn't really have the personell for a 3-4. However, that is still the abse system that he wants to use, and he wants the players to get used to that kind of scheme. However, I think that like most good coaches, he will adjust to what will give the team the best chacne to win. We know that in mature form we can expect to see the Jets using 3-4, 4-3 and any number of other fronts as well. For the time being it's mostly 3-4, but once the staff feels like the team can execute 3-4, they will begin to go with other fronts as well. Therfore, I thinkn the Jets could actually have worse results later in the season on defense, as they mix in more and more packages and fronts.