OK, just because a pokemon sometimes carries one move that can beat you, doesn't mean you instantly aren't a counter. Heatran can still switch into every single other move that Skymin has except Earth Power, that is a pretty solid counter to me. Lots of Skymin do not even use Earth Power. That's like saying Cresselia isn't a good Garchomp switchin because its 2hkod by CB Outrage. In d/p, most movepools are expansive enough to the point where its counters can be hit reasonably hard. Lickilicky can use Fire Blast on Bronzong, Gyarados has Taunt, Swampert uses Ice Beam, etc. In d/p, countering is almost always cut down to a point where its "good enough" since lots of sets require seeing every move...which means taking hits. Heatran certainly falls into a category where it's "good enough of a counter" to declare it one, stop getting so hung up on technicalities (since so many people seem to agree that presence of counters is not a qualification for uber status).
"one ko is guaranteed" is blatantly false. I got to #4 on the OU ladder at one point and i've only lost one pokemon to Skymin to this point (to a crit). My team that is completely unchanged from d/p to platinum has no issues with it. There were already very common OU pokemon that counter Skymin at the time of its introduction, I'm not sure why people see it as a threat at all...can we please stop overhyping Serene Grace? lol
This is complete garbage. Nothing you said is right.
According to the typical movesets page, Skymin's is Seed Flare, Air Slash, Earth Power and Substitute. No others are mentioned. Heatran cannot swap into Earth Power and Substitute., 2 out of 4 moves.
And when was Cresselia a Garchomp counter? Yache Berry Chomp sets up a SD, then 2HKOs while Cresselia doesn't OHKO thanks to Yache (and like you said, Cresselia can't swap into CB Outrage, but that's completely irrevelant).
A counter applies to the moveset of the pokemon. Heatran is a check, but not a counter to the generic Skymin (and Cresselia is not even a check for standard Chomp). The definition of a counter is, as stated by smogon, a pokemon that can switch safely without reasonable threat. Heatran faces a OHKO threat by two of Skymin's moves. (Oh, and by the way, many Gyarados have Taunt and many Swampert have Ice Beam).
Counters was one of the reasons why Garchomp was declared uber (not the only one, but it was one).
#4 on the OU Ladder before plat is irrelevant, and I doubt you didn't have any issues with plat changes. Leads have changed lots thanks to Trick. And Skymin came out with the plat changes like Bullet Punch Scizor (a check, not a counter) and with the increased popularity in Scarf Heatran (in addition to the increased popularity from Chomp moving into uber).
Skymin is mainly about prediction, not luck. Heres some damage calculations against some of the top OU pokemon, by a 339 SpcAtt Skymin (standard). This assumes the generic moveset of Seed Flare, Air Slash, Earth Power and Substitute.
If Heatran attempts to swap in, Earth Power or Sub can lead to a OHKO withou SR damage.
If 252 Hlth 0 SpcDef neutral nature Scizor swaps in, LO Seed Flare followed by Air Slash KOs without SR damage.
If Zapdos swaps in, LO Seed Flare with Spc Drop followed Air Slash KOs 252 Hlth 0 SpcDef neutral nature Zapdos with SR damage.
Metagross with 252 Hlth, 0 SpcDef neutral nature gets 2HKOed by Earth Power without a LO boost.
Air Slash, without LO and SR, is a 2HKO on 4 Hlth, 0 SpcDef neutral nature Gengar and Lucario.
If 4 Hlth, 0 SpcDef Salamance swaps in on non LO Seed Flare and has a SpcDrop, Air Slash then KOs
without SR damage.
Gyarados with 164 Hlth EVs, 0 SpcDef, neutral nature is 2HKOed by non LO Seed Flare
without the SpcDrop and without SR damage.
252 Hlth, 4 SpcDef neutral nature Tyranitar gets OHKOed by LO Seed Flare with SR damage.
These calculations are absolute; they will occur 100% of the time. So any smart Skymin user should get at least one KO, and none of the above pokemon can safely swap into Skymin without proper prediction. And if Skymin sets up a Sub as one of these swaps in, only Scizor and Scarf users can beat Skymin (Scizor requires Skymin to have taken SR damage or he fails too).
And none of these calculations required the need of Air Slash flinch. Most didn't even need a Seed Flare SpcDrop and a LO boost.