While true, you have to keep in mind this isn't a be-all and end-all game for Square-Enix, but rather a port of a PSP game. The soundtrack was designed for a game that was designed to be released in a single region. Now that it's going global, I can hardly imagine they would redo the soundtrack from scratch.
I agree that variation is great, but if you sit and listen to a soundtrack then you will find that a lot of games re-use themes a lot of the time, and that's just the result of listening to each track once. When you play a game, you notice the re-use of the theme but as other songs are played more often than once, the breakup of said songs becomes more tolerable. I would never say that VII overused the theme or even got close to it, because of the other awesome tracks that were very important. If every single track that doesn't use the theme ends up being used only once, then sure, that's something you could be annoyed about. But for all you know, one of those other songs that didn't use the theme is akin to Aerith's Theme, Gold Saucer, Those Who Fight or the Turk's Theme, and get played a lot as well to help break up any repetition.
This is why I generally play games before I listen to soundtracks. ;)