Nah the F-18 is the closest thing to a proper old-school fighter still around, close to the F-14 at least, so for movie purposes it makes sense. The broken turd that is the F-35 is really not much cop and wouldn't be particularly exciting in a movie, the focus on stealth wouldn't fit. Plus the f-18 is a 2-seater, allowing callbacks to the original, while I think the F-35 is single-seater. F-22 is also single-seat, so that may explain ruling that out.
In other news: Please please please be awesome. Top Gun is one of my all-time favourite films, for the soundtrack alone let alone the sheer awesomeness of the film, a part of my childhood that means a lot to me and made me love motorbikes and fighter planes.