Here's the thing. For the most part, Speed EVs are based on speed benchmarks. Skymin represents the top benchmark in OU outside of Aerodactyl, Crobat, and Jolteon, which means that beating it is significant- you also beat everything else. Garchomp was a special case. Stuff like Starmie would run specific EVs for Garchomp because it was meant to be a Garchomp revenge killer / check. Remember that a ton of stuff used to be all about "outspeeding Adamant ScarfCross after +1" back in the day? Heracross isn't broken, now is it?
The idea that something with a new speed tier forces new speed benchmarks isn't ridiculous. It's actually pretty standard for a metagame. As for damage calculations, well, Skumin is weak to SR, so as long as SR is up its MHP is 75% (Garchomp RESISTED Stealth Rock), which means that hitting specific "killing Skymin" targets isn't actually a major aim.
As for what I think of Skymin? If it had something like Nasty Plot or Tail Glow, THEN I'd think it was broken. Garchomp wasn't broken just for hitting hard. It would stat up, survive with Yache, then HIT REALLY HARD. Skymin doesn't have the raw power (120 versus 130 Base SpA/Atk stats), nor the raw move power. Garchomp had a Base 120 STAB and a base 100 STAB, both in PHENOMENAL attacking types, both 100% accurate. Skymin has a Base 120 STAB and a Base 75 STAB, both in kinda mediocre attacking types. On top of that, they both have less than perfect accuracy, meaning a miss can ruin your day. Serene Grace is simply an overhyped ability. Togekiss is GREAT with Paraflinch for one main reason- When it does fail, Togekiss is still bulky enough to take the hit and keep on truckin. Skymin lacks that, so for the most part, if it doesn't flinch, it's dead.
Let's look at other sets. It can SubSeed, you say? Other things can do it FAR better, and have been doing it far longer than Skymin. Breloom, Celebi, and Sceptile all come to mind, and those sets aren't anything near broken. Substitute sets are kinda iffy too. The common set is going to be Seed Flare/Air Slash/Earth Power/Substitute. By the time you've come into SR and set up a sub, you're already at 50% HP. And that's only if your opponent LETS you set up a sub. If they break it, then you're at 50% HP with no sub, and will probably have to switch out, ruining the rest of your Subbing days.
Let's look at counters. Sets without Earth Power are rocked by Heatran, sets without HP Fire are rocked by Scizor, and pretty much every set gets walled by Bronzong and Blissey. Dragonite can come in on non HP Ice sets, resist Seed Flare 4x, and OHKO with pretty much any SE attack while not getting flinched due to Inner Focus. Mamoswine, Weavile, and Donphan all carry Ice Shard, a 4x effective attack. So what if Donphan's isn't STABed. SR has probably chipped off that 25%, which means it's now strong enough to put Skymin out of commission. Regice has nuts Special Defense, Clear Body to negate drops, and STAB Ice attacks to put Skymin down. Registeel resists everything but Earth Power/HP Fire, has the same Clear Body, and has Ice Punch to finish off said Skymin. If Skymin happens to catch a Thunder Wave from the likes of Blissey or Celebi, then it's permanently out of commission (Garchomp was immune to TWave). Pretty much every counter to Skymin with the exception of Dragonite and the Regis was high OU before Skymin popped up.
Skymin has also done a great deal good for the metagame, IMO. It's probably the most efficient way to combat Bulky Waters ever to appear in Pokemon, with high-powered STAB Grass attacks and a good Special Attack stat to back it up. The biggest effect from this is that it gives a minor boost to Offensive teams that had problems breaking through walls like Swampert. Sure, Shaymin-G had the same powerful STAB move, but it had a terrible movepool, mediocre offensive stats (100/100/100 just isn't cutting it), and the complete inability to hurt anything that resisted grass (read: a shitload).
Oddly enough, the most effective set I ever ran was a completely ridiculous one unheardof when Skymin first arrived on the scene: Choice Scarf Skymin. The upsides are endless. Earth Power beats +Speed Heatran expecting to outspeed me. Air Slash can flinch the hell out of stuff given enough luck. HP Ice eliminates Salamence, who I now outspeed even after a DD. Seed Flare also takes out Tyranitar, even if it gets 2 DDs. It also smacks Gyarados even after a DD. And way back yonder in that speed-infested metagame, Modest Scarf Shaymin-S outsped Timid Scarfgar and lead Deoxys-S, which meant that Deoxys-S would get at most Stealth Rock and nothing more, and nothing at all if I flinched with Air Slash. Trick Gengar would also often try and drop its Scarf on me only to see me outspeed and him get another scarf in return.
All in all, I think Skymin has a positive effect on the metagame. It's powerful, but not out of hand, and it has the strength needed to put the completely overused Bulky Waters in their place. It's not overly defensive, it's strong but not too strong, it has no reliable boosting move, and the majority of its hard counters are all high OU already, so it's not really centralizing the metagame around itself.