In response to all of that:
1st of all: Magmortar
Why it has Solarbeam and Hyperbeam: I'm not sure why, but I encounter a lot of pokemon that use Protect and Detect a LOT. Solarbeam is okay for that. Plus, I have 7 pokemon that can use Sunny Day. I only use Hyperbeam for quick knockouts. I don't need Thunderbolt since I already have Solarbeam. I don't like Focus Blast that much because it has low accuracy. Undecided
Hyper Beam may kill quick, but the recharge turn can, and most likely will, screw you. It doesn't even let you switch out. Easy opportunity for a sweeper to come in and use Swords Dance/Nasty Plot during your recharge turn. Hyper Beam has now just screwed you. Granted, a Focus Blast miss could screw you similarly, but at least with Focus Blast there's a fairly good chance of not being screwed over, unlike Hyper Beam DEFINITELY screwing you over. Plus, Focus Blast will put Blissey in its place (Hyper Beam won't,) and any Special attack that can put Blissey in its place is well worth having in my opinion.
Also, in what way is Solarbeam good against Protect and Detect? The way I see it is, Solarbeam charges up, opponent uses Protect, Solarbeam does nothing. Even Solarbeam + Sunny Day is a poor combo since it baits Fire-types to switch in and Solarbeam won't be hurting them much. It will also bait in an opponent's Tyranitar (which are extremely popular) to murder the field with its Sand Stream, and since Solarbeam's power is halved in a Sandstorm (as well as getting the charge-up turn back again) and T-Tar's Special Defense is boosted by 50%, well...enough said. Also, since Tyranitar resists Flamethrower, Hyper Beam AND Psychic...just gets worse. T-Tar also happens to be 4x weak to Focus Blast. *hint hint*
2nd of all: Metagross
Why I like its current moveset: I give it a Shuca Berry because it is not very fast. So if it gets hit by a Ground-type attack, it will have enough HP to use Magnet Rise. Same goes for Magnezaone. Hammer Arm to make it slower(I have some other pokemon that can use Trick Room) And Psychic to take care of pokemon that like to use Counter a lot.(Which I have encountered a lot recently.)
Trick Room is a rather poor move, since it helps opposing defensive Pokemon use their nasty status/hazing/healing moves, and god help you if your opponent has a Snorlax. Psychic is viable since it isn't that bad on Metagross's Sp.Attack, but in my opinion there are far better ways of dealing with Counter (Status Moves.)
3rd of all: Gyarados.
Why it has special attacks: The same reason as Metagross's Psychic. For pokemon that like to use Counter. And if a pokemon decides to use Mirror Coat, then the counterratack won't be so great since Gyarados's base special attack stat is low. Also, I would like to point out that Gyarados is sort of a support pokemon as well as an attacker. Flamethrower can burn an enemy and Thunderbolt can paralyze an enemy. And Waterfall is the move that it almost always uses(Reason for Mystic Water). Also, I'm not really that afraid of Dragon-types against my Gyarados because I already have other pokemon that can deal with dragons.
Gyarados is in no way a supporter since although Flamethrower and Thunderbolt can indeed burn/paralyze, you're looking at a 9.8% chance of doing so either way, and rubbish damage on both 100% of the time. Yes, I agree that is support...for your opponent, that is. Also, if you plan on using Waterfall all the time, Choice Band's 50% power boost trumps Mystic Water's 10% boost. Also, Pokemon with Counter/Mirror Coat are very rare - only one I can say I've seen recently (besides Wobbuffet) was a Blissey with Counter, and it just ended up getting OHKO'd by the attacks it was trying to Counter. The only thing your Gyarados's Special attacks will do is give your opponent ample time to blast you with a Thunderbolt. If Counter worries you, use Dragon Dance to increase your Attack and thus increase the odds of getting the OHKO that would render Counter useless. If you want your Gyarados to play a more supportive role, the best move to have is Taunt.
Last of all: Magnezone
Reason for why it is how it is: Magnet Rise-good for evasion. Shuca Berry-good for preperation of Magnet Rise. I keep Discharge because Magnezone is always partnered with Garchomp. First Magnezone uses Magnet Rise. Garchomp uses some other attack besides Earthquake if Magnezone has not yet used Magnet Rise. Then Magnezone uses Disharge which hits both opponent pokemon and does not damage Garchomp since it's a Ground-type. Then Garchomp uses Earthquake which also hits both opponent pokemon and does not damage Magnezone after it uses Magnet Rise. I also gave Magnezone Magnet Bomb to get rid of pesky evasive pokemon. And...I really wanted to teach Magnezone Flash Cannon but I accidentally taught it to my...Aggron? he he he awww man I am sooo embarrassed I had to share that... Embarrassed
The damage reduction caused by Discharge hitting everyone is not worth it, same with Earthquake - although you will be doing severe damage to both opponents, odds are you won't be killing either of them, which gives them ample time to use two strong attacks on one of your Pokemon which will definitely kill them off - this gets even more ugly if the opponents are faster than you, and with a Magnezone they most certainly will be. Although Magnet Bomb doesn't miss, it's also about as effective as any Special Attack is by Gyarados, i.e. not very, so those "pesky evasive Pokemon" will hardly be running for the hills. Magnet Rise is viable, I'll agree with that. As for Flash Cannon, stick in a second filler move - Magnezone has plenty.
Everyone has reasons for making their team the way it is. However, your reasons are flimsy at best. There's no point in putting Special moves on pure Physical sweepers and vice versa just to avoid Counter/Mirror Coat because not everyone actually uses these moves, and against an opponent who doesn't use Counter/Mirror Coat (who are in the majority) your movesets will be much less effective. As for Hyper Beam and Solarbeam, there's no defense for using either, not even Sunny Day. There are plenty of moves that are vastly superior to the both of them, and they're not hard to find.