Here is the deal:
-In the eyes of Bupers, you are an FA-18 pilot. Although the C is a different platform from the E/F NATOPS wise, you can easily transition between tours. In other words, you can do like me, fly Charlies for your fleet tour, then teach at the E/F FRS, and be wide open for C/E/F for all tours. At your stage, certainly don't try and game it career wise, your first tour won't matter too much down the road. Also, the JSF is so far off you have no chance of flying it on your first tour.
-The planes fly nearly identical. The E/F has a few improvements in certain areas, but nothing dramatic. The C flies a little more nimble in certain areas, ditching, or visual bombing. It's a wash in my opinion.
-The E/F has a ton more gas and bringback, which is huge for the boat. I would welcome not having to show up bingo on the ball like we often had to do in the legacy. The downside of the extra gas of course is that you fly a lot of tanking missions (a lot of folks don't mind or actually enjoy the tanking). If I were to stay in and go back to the fleet, I would want the E/F simply for the extra gas, if nothing else.
-Like someone said, 122 and 106 train differently. At 106 you select E or F very early in the FRS and are trained that way. We used to do that at 122 but found that we were making lazy F pilots. The F guys got so used to relying on their intructor wso's that they became lazy. Also, there was a tendency to stick the weaker students into the F pipeline. About a year and a half ago we started training everybody to be single seat and then let them select just before the boat. This is making much stronger pilots across the board, as their instructors are now more of coaches/observers and can't carry the load for a weaker student. The counter argument (largely favored by old tomcat folks) is that the F guys leave the FRS without a true appreciation for the crew concept. I disagree, but there you go.
-An interesting observation I have made is that most pilots, when we had them select early at the FRS, wanted F's. Once we changed our syllabus to train them single seat the majority of pilots wanted single seat for their selection.
-As far as the single vs. two seat, well there are perks to both. I think I could happily go back to a two seat squadron, but I am glad I flew single seat for my first tour. There is a certain amount of pride in being able to do everything for yourself, and it is the only single seat plane left in the navy.
-Most instructor pilots who leave the FRS for a follow on tour prefer to do what they did in their first fleet tour. If they flew single seat they almost always want to return single seat, and vice versa.