Im afraid I have to Disagree. First of all we are on the stats thread so:
Yeah Metal Sound is extremely uncommon, so "Everything is beaten by this set but nobody uses it" isn't really a viable arguement. Metal Sound is easily taken down by anything with 80+ Base Speed and Earthquake. Mamoswine, Flygon, Salamence, Gyarados, <Insert Pokemon on offensive team that knows Water/Fighting/Ground move with 80+ Base Speed>. Yeah so MS set doesn't really do much as long as you have a Pokemon with Earthquake (Which im pretty sure is one of, if not the, most common move). So please dont say a set that is rarely seen as a basis for a Pokemon being uber, especially when that set still falls flat to countless Pokemon.
Second, being "versitile" in no way makes a Pokemon uber. Honestly, Heatran are seen as either a Lead or some sort of attacker with Earth Power/Fire Blast/ <insert HP>/ Explosion/Dragon Pulse. Not very versitile, in my opinion, its just viable with different items. By the "versitile" arguement Jirachi, Celebi, Infernape and many others would be uber. Also, I fail to see how having 130 base special attack and having the move Stealth Rock is a valid arguement for versatile.
You only think there is one counter? Lets see a list: Suicune, Vaporeon, Gyarados, Aerodactyl, Flygon (somewhat), Blissey, some Starmie sets, Snorlax, Tyranitar. All of these wall you bar Explosion, and the HP you choose lets you deal with some, but not others.
Also, if you are going to keep your arguement up, please at least address the part of your quote I bolded, because that statement is so wrong. Thats like saying this Pokemon is uber because 1 Pokemon cannot wall every single one if its moves. That in no way makes a Pokemon uber. Most Pokemon have sets which force their way through normal counters, but lose to Pokemon they would normally take out. For instance, Spec Lucario. Im not trying to insult you here, but I fail to see how one can consider Heatran Uber...
The Metal sound set does have counters, I agree, things faster and have Earthquake/close combat/waterfall/super effective move. Now, I will address some of the "counters" you have listed.
Suicune-The metal sound set handles this, after a Metal Sound, Hidden power Grass does 87-100% to a 252 HP / 0 SpD Bold Suicune with Life orb. Heatran many times will also a Passho berry to take a surf and KO back. Specially defensive sets can also take it on. Torment Tran can stall it out, with Toxic spikes, if it doesn’t have rest.
Vaporeon: Really the same as Suciune, however a little easier, as HP Grass will do slightly more. Specially defensive sets can also take it on. Torment Tran can stall it out, with Toxic spikes.
Gyarados: Gets utterly crippled by WilloWisp, HP electric will OHKO the thing. This is one of the most difficult Pokemon to face though. Explosion is a last resort, though. Providing it switches in on a metal sound, it gets beaten, SR also hurts it.
Aerodactyl: Again, Willowisp will cripple the heck out of this Pokemon making it almost useless. To note, almost all Aerodactly are leads, 88.5% of the Aerodactly had Focus sash. It is very rare, outside the lead position. HP electric, will also give this Pokemon major hurt.
Flygon: Willowisp cripples it, to the point it’s almost useless, except for U-Turning/scouting. It has to be wary of switching on a dragon pulse. To note, a Willowisped EQ will not OHKO Heatran, and Heatran can do massive damage back with Dragon Pulse.
Blissey: Gets murdered by the Metal sound set, a timid Life Orb, Fireblast does 46%-54%, and 2KO after SR. Torment Tran can stall it out, with Toxic spikes.
Starmie-Easily gets screwed over by Scarf sets, Again Metal sound makes sure HP grass/electric or even Fireblast OHKO, the Specially defensive sets can also take it on.
Snorlax-Woah, quite a hard one, Metal sound and Willowisp can make it life miserable, Explosion could be used a last ditch effort, if needed. Torment Tran can stall it out, with Toxic spikes.
Tyranitar-Willowisp or Metal Sound sets cripple it to the point where its almost useless. Shuca berry variants can get a hit or two on it to. Torment Tran can stall it out, with Toxic spikes.
Mamoswine-Well, this Pokemon can't safely switch in, Fireblast will easily OHKO. Other than that, Willwisp will cripple it.
Okay, now were getting to versatility. Heatran can fill numerous roles, it can be Revenge Killer, with Choice Scarf, it can be a reliable Phazer/Sleep Talker, it can be good lead, It can be a insanely powerful, attacker with choice specs, a great team supporter with the Heatrap set, made to specifically lure Pokemon in and KO them. Some of the numerous moves that it uses effectively are Stealth rock, Fire Blast/OverHeat/Lave Plume/Magma Storm, Earth Power, Dragon Pulse, Explosion, Roar, Torment, Taunt, Toxic, Substitute, the various Hidden powers, Willowisp, SolarBeam, Sleeptalk, rest, metal sound and protect. That Base 130 special is tied for highest out of all OU, (barring Porygon-Z, Alakazam, which are rarely seen anyway) Flash fire, and its good bulk provide it numerous opportunities to switch in. It is probably one of the best, if not the best Pokemon to force switches in OU. In terms of stats, it has a BST of 600, is tied highest for the highest in OU(barring Reggigas, Slaking who are rarely useful and are unseen.) Specs Lucario, is rarely seen, and however it can't switch Scarf Heatran easily OHKOes. Also a Heatran with 252HP/252 Sp. Def and a calm nature will survive a attack and OHKO right back, just to make a point. I never said that I thought Heatran was a Uber, I said I thought, excluding Salamence, Heatran is the Pokemon closest to being up to Uber standards. It may have numerous weaknesses, but the points I am trump that almost completely. It’s up to #2 on standard, #1 on suspect with an amazing 37.56% of teams using it, well above the #2, Rotom-A at 29.26%, and huge 8% difference, and 12% off of #3 Gyarados with 25.41%. Depending on the suspect tests, it may actually over take Scizor as OU's #1 Pokemon. Scizor has been #1 for almost 2 years, and for a couple months before Heatran was the #1 OU Pokemon. I think usage stats speak for their self; Heatran is one heck of a Pokemon.