Flygon and Swampert both gets STAB on Earthquake, so keep those;
Gardevoir may need a ghost type for coverage but Shadow Ball is a physical move in Gen 3, and Gardevoir has pathetic stats on the physical side. I'd switch it out for Thunderbolt and switch Shock Wave for Thunder Wave - always handy to hax the opponent.
Hyper Beam isn't really that good on Flygon, in fact, I only use it on Slaking since you're vulnerable for the next turn. I'd probably switch it out for Fire Blast for coverage against grass types.
Skarmory is an great staller, so keep that - Milotic would have been better though, but you can't get it until much later. I would teach Skarm Rest instead of Steel Wing (Steel sucks for attacking) to make him last even longer
Camerupt has a huge gaping weakness to water so I wouldn't keep Amnesia on. There isn't any good fire types in Emerald that I could suggest so keep it I guess. I personally prefer Fire Blast over Flamethrower but the latter IS a bit more reliable. Definitely switch Magnitude to EQ. I wold also consider Strength since you need the HM to get through the game anyways.
Hi and I am a signature. Here's my opinion's on the:
Anime: Kanto > Kalos > Sinnoh > Johto > Hoenn > Unova (Origins: 6/10)
Movies: Johto > Kanto > Hoenn > Sinnoh > Unova
Anime music: Sinnoh > Hoenn = Johto > Kanto > Unova > XY
Games: GSC (HGSS included) > XY = RSE = RBGY > DPP > BW