Three factors.
What squadron will be taking someone from your class/opposite coasts class and is there a Pri A requirement for that squadron. Basically needs of the Navy. This one trumps the next two.
What would you like. Preference sheet that you fill out.
What the IP's, Class Leaders and Training O think about you and your ability to work with someone else in the jet. If you are a pilot, you will be trained from the beginning to fly single seat. The question isn't can you fly alone, it's how well you work with others in the jet. There are some people out there that just suck at this. FRS IP's and IWSO's have a good feel for who they are. So, do not think that all the rock stars will be single seat dudes and those that need help go F's. The syllabus doesn't work that way. If you make it through to the point where selection comes into play, you will do fine in either E or F. The big question is "how well you play with others".
As far as mission differences, there are just a few. FAC/A being the main difference. The Navy does not allow single seat A/C to perform this mission. The other used to be the armed recon or SHARP pod mission. This is a moot point as the SHARP pod has been taken away, at least it had a year or so ago. It may be back now, and if so, my apology. Also, I do believe that there was a West Coast E squadron that flew the mission. However, the majority of the Reece missions were given to the F squadron in the air wing.
There are also things two people can do in a high lot F that single seat guys might not. An example would be that a WSO could be using the A/G mode of the radar while the pilot uses the A/A mode for sanitization. This would allow the WSO to do some good work in the back, distribute info to the rest of the flight in high work load environments whereas a single seat guy will start task shedding some duties. It's all about prioritization. The new jets have so much info available that, at times, one guy can't process it alone. With a good crew 1+1=2 and twice the work can be done, ie FAC/A. However, depending on the crew, sometimes 1+1 < 2. Where two guys working together are a detriment to the mission and one guy would be better off. It's all about crew coordination and the personalities involved. For me, it was nice having someone else in the jet that wanted to live just as much as I did. Especially night strafing in the mountains or helping to look over your shoulder for some wild card. Hell even in BFM now days when your WSO has a JHMCS and can lock someone up for you in a fur ball and make watch the deck calls if need be.
When I selected, I looked at other factors. For me it was about QOL. In a squadron, if you have twice as many people, it's half the work. That allows for more play time. Twice the JO's meant less standing of SDO, more help in mission planning, burrito runs, etc. I was looking at quality of life both at home and deployed. Our single seat sister squadron JO's that were not LSO's were standing duty weekly if not more often. In our squadron, non LSO JO's were standing watch once every two to three weeks. Camaraderie also seemed higher the F squadrons. It just seemed to me to be a more relaxing atmosphere. The singles seat guys always seemed to be working there asses off. I'm not saying that they didn't have a great RR. To me it seemed like they were always on the go. Whereas in the F squadrons, you could take a breather every once in a while.
Anyway, that's my two cents as a fleet F guy, FRS IP and soon to be E DH. Any other fleet C or E guys please feel free to chime in on your thoughts. Also, you can debunk any of my F ism's about life in a single seat fleet squadron.