Be warned: These are just my opinions, and I would love to hear yours below. I am NOT saying JMU can't win it all, just that they probably won't and another, more complete team will. I intend this post only to spark discussion about JMU's weaknesses going into next season.

1. The QB Question. It's a pretty obvious problem that the QB room at JMU doesn't have a clear path forward. A question at Quarterback is one of the hardest things to solve for a team, especially a team who's going through a coaching change.
2. The coaching change. There's obviously something to be said about having a new coach being difficult, for a multitude of reasons. There's also something to be said for the fact that JMU made a successful coaching change in 2016 and took the national title. What's different between 2016 and 2019 is the experience that the coach is inheriting. The depth of experience JMU has right now certainly makes it easier to rely on players to play strong and perform on the field. But experience can also be a detriment during a coaching change if it shakes up the team dynamic. Cignetti is going to come in with a "blueprint" like he did with Elon, and younger players are arguably easier to have "buy into" this gameplan. Elon was mostly a young team when Cignetti came in, and as a result the young, hungry players were eager to get their chance and would buy into the gameplan eagerly. Given the QB battle they have going on, they could get 3, perhaps even 4 QBs vying for the top job, and whoever gets the position will want to show that they deserve the spot. And given the lack of reliability at QB, a person in that position who both isn't proven yet and also feels they have to prove themselves is a bad mixture. And Cignetti loves to run the ball. He's practically addicted to running right between the tackles. This might not sit well with a QB room full of guys that feel they need to prove they can take up the mantle, and it might lead to more mistakes when they do throw the ball. We all saw how badly JMU can be when their QB throws interceptions by last year's UNH game.
3. JMU doesn't ostensibly have a true "leader" in the team right now. Key word here is "ostensibly", meaning that if they do it's not publicly known or obvious. If they do, cool. But from the outside it doesn't seem like they have a true person to rally around like Bryan Schor was. Schor was reliable and charismatic. This point is both the most important and the most shaky for me, because none of us really know the atmosphere in the locker room, not really, so it could be moot. But during a coaching change JMU is losing its one ostensible leader in Mike Houston, who really seemed to keep the team's morale and passion where it needed to be, up until near the end when he was leaving. But JMU struggled last year against good teams, which is my next point, and it seemed to me because they didn't have a leader on the field they could rely on. DiNucci just didn't perform consistently well under pressure and I think this was the biggest thing that contributed to the team's losses to Elon, UNH, and Colgate. In 2016 I think what helped JMU win the national title and perform against good teams was more about Bryan Schor, not Mike Houston, and I think this team needs a leader on the field to be successful. It remains to be seen if someone like that will stand up.
4. Something held JMU back last year when playing against "good" teams. They beat the crap out of "bad" teams. But they seemed to falter when pitted against teams that really challenged them. We saw this first in the Elon game, where they just didn't have an answer for our running game and that opened up the pass over time (even though Elon's QB had a very mediocre game, the ability to pass on the last drive and the performance on the last drive in particular was what helped them win the game). I'm not sure what held JMU back in this game, but it seemed like they just faltered when they couldn't run the ball against Elon's defense. Given a coach that loves to run the ball, they might struggle if they can't make that side of their game work, and that in particular might make them one-dimensional.
5. Cignetti runs the ball first and foremost. JMU has been no stranger to running the ball, and they will be good at it, so this is the weakest of my criticisms of their new scheme, but I still think JMU will not show very much confidence in their passing game, trying multiple QBs before deciding on one, and even after that will be one-dimensional.

Caveat - The biggest reason they might win actually it all that I don't see talked about:
Every single starting OLineman returns for JMU, and they are all beasts. This will synergize well with Cignetti's preference for running the ball. If JMU can dominate the line of scrimmage, there's very little anyone can do to stop them given their talent at RB. It might not matter that they become one-dimensional. If they can run the ball as much as NDSU does and still succeed, then there's no problem. Now, they probably won't have a QB like Easton Stick to open up the run game. But if they do get something good going there, they can be potent in the run game.