Please use the Help thread sticky at the top of this section for questions please, and only after looking at the FAQ sticky thread right below it as well. A lot of info about the games is within that.
But as for your qustions here - only 'major battles' you can do are against the E4/Lance again, your rival, gym leader rematches (Johto and Kanto) and Red (Mt Silver, reappears each time you beat the E4 + Lance again). And legendary Pokemon I suppose 9again, FAQ thread has a list on those). Sinnoh gym leaders cannot be battled although a couple do make cameos.
Answered, so closed.