I graduated from USNA this year (2017), went USMC Air and am nearing the end of TBS. I can't speak for c/o 2018 like BDHuff09 can, but I he brings up several good points. Here's what I view as the issues.
On PROTRAMID, several Navy pilots attempted to persuade mids who were debating going Navy aviation versus Marine Air by telling them that Marine Corps platforms were "held together with duct tape." Those types of conversations, along with a number of recent mishaps, certainly play a role.
The family issue is a big one as well. A lot of mids may be gung ho for a couple years, but if they are in a serious relationship (or just hope to be in one in the near future) and are thinking of marriage, the Marine Corps can seem less attractive. While the Navy can be hard on relationships as well, it's no secret to mids that Marine Corps officers on the yard are often there earlier and later than their Navy counterparts, and carry that kind of commitment to their job elsewhere.
An ongoing issue is that those who want to fly tend to go Navy and those who want to be Marines go ground, often hoping for a combat arms slot. The length of TBS, which delays the start of flight school certainly factors into this to some degree. I think this could be at least partially addressed by Marine Corps pilots stationed at USNA talking more about their experience in combat, supporting guys on the ground. An officer currently at USNA played a role in me choosing air vs ground by talking to me one-on-one about his experiences in Afghanistan doing Close Air Support (CAS) missions. Many mids attempt to get Marine Corps due to its reputation as a lean, mean, fighting organization. If USMC pilots at USNA are proactive in talking to mids about how their roles directly affect say, an infantry company in combat, more of those interested in USMC Ground may wind up opting for Air.
In my opinion, the USMC officers at USNA have been top-notch and are often highly respected among mids, even if the occasional one isn't well liked. When several classmates and I were discussing the shortage of Marine pilot hopefuls, one issue a classmate of mine brought up was the issue of "cycles" of sorts happening at USNA. From our observation, it seems as though the classes that wind of leading/training plebe classes often have a big effect on them. Thus, a class that has a high number of motivated members become Marine may wind up influencing a class several years behind them to do the same, and vice versa. In my company at least, the class that training 2018 was not a USMC-motivated class, and the fruits of that are seen in 2018 in my old company now. That's purely anecdotal, but it may have a shred of truth in it.