The team looks good so far. I'd just replace Protect on Swampert with a different move. In general Protect doesn't really do much, just stalls a turn and take up a move-slot. You also don't have anything with Leech Seed or Toxic so stalling turns is of limited value. Curse, Mirror Coat, or Rest are good alternatives, although you need to breed for Curse and Mirror Coat. Mirror Coat requires breeding with Corsola, whilst Curse requires breeding with Slowpoke (or breeding from Torkoal => Rhyhorn => Swampert for Emerald only). I think your team might benefit most from Mirror Coat to deal with the Lati twins, who are very difficult to deal with for your team.
Master balls are the cheapest thing ever invented. It's more fun catching everything with balls that can fail. 'caught Latios in the wild without master ball ftw'