If you go to an academy and you want to switch you'll need a damn good excuse. Rivalry among the branches is pretty tense and if you leave, everyone who helped get you in the academy (congressmen / LOs / administrators / etc.) will feel slapped in the face. Not to mention the friends you've made there.
Also, I'm going with an AFROTC scholarship this year, but I was seriously considering the Marines for a while, so I did a decent amount of research. I found it is very hard to get a marine jet slot compared to the AF (over 60% of their fleet are choppers). I mean, there are some classes that go through flight school just to find 1, if any, jet slots that are open. Of course, being a Marine in itself is awesome, but if your main goal is to fly fighters, then go with the AF. If you want to crawl through the mud and blow #### up, then go in the Marines. I think the best way anyone put it was "In the navy or AF you're a pilot, but in the marines, you're an infantry officer who happens to fly." Also, I talked to a CH53 pilot at Miramar about a month ago, and he said that Marines just do not get the flight time that the other services do. And keep in mind that the Marines are a department of the Navy, so go to this link, scroll down, and read the post by the webmaster
http://www.airwarriors.com/forum/showthread.php?p=66874#post66874 It's long, but it's well worth it.
Good luck