Here is a good strategy to beat the E4 and Champion. Before you face the E4 capture Rayquasa (if you haven't already) and has the move Outrage already learned. This is the bread and butter for beating the E4. Once you have him caught make him learn Thunderbolt, Icebeam, and any other move you want him to learn (I find Dragon Claw, Blizzard, or Thunder is helpful). After that fly over to the Daycare center, store Rayquasa, and wait for him to reach level 85 (85 is preferred, but anything that is 83+ is okay). Once all of that is done you can face the E4 using only Rayquasa and you'll get at least to Ice gym. Just spam outrage to nuke down the first 2 guys (you'll want to earn some exp for some additional levels to help you out). When you face the Ice gym use your fire pokemon (or if your not using a fire pokemon, then have Rayquasa learn Flamethrower or Fire Blast) and use Thunderbolt to kill her water/ice type pokemon. Once that is done the dragon type guy should be easy and you'll face the Champion.