http://www.youtube.com/watch?v=3NcUyJxiOdo ^ I mean the non-cool version of it, the normal version and...the one that's been featured at the end of every major X/Y trailer, actually (eh, you know, the "du du DUN du du DUN"...thing...)
No seriously, I've heard it so many times...I'm very tired of it. Just look at THIS http://www.youtube.com/watch?v=zUfp8np0F6s and tell me that opening wasn't great until the DANANA started, it's just...ugh... I know I'm complaining over a very simple thing, but still, It's not as iconic as Fire Emblem's or Mario's or Zelda's (even though those these two don't really have a 'main theme' per se, unless you consider World 1-1 and Hyrule Field as their main themes). Hell, I would be completely okay with "I wanna be...the very best..." being the main pokémon theme, it's so much more iconic.
Pokemon's main theme is one of the most iconic songs in video games, imo. It first appeared as Red and Blue's opening (http://www.youtube.com/watch?v=NdJQopRuH1E) and has been remixed for every generation of Pokemon, if I remember correctly. I'm pretty sure it's not going anywhere. But I can see why you're getting tired of it.
BTW, Zelda definitely does have a main theme: http://www.youtube.com/watch?v=8-mNw11ZXbY
I'm pretty sure it's part of the overworld in the early games, but it has appeared in some form in every game in recent memory as a "main theme".
Official Something of Somewhere http://i.imgur.com/83ZkrSm.jpg