I think people are stuck in this idea that simply having counters makes you an irrevocably balanced Pokemon that shouldn't be considered for banishment from the tier. You have to consider how many of them even exist and whether or not they're truly viable in their respective metagames. Cresselia, for example, was largely ignored as a counter for Salamence due to a large number of factors that outright booted it out of OU. And plus, it was just one Pokemon. Cresselia being a mandatory addition to every team that doesn't want to lose to Salamence is a high signifier of unbalance.Furthermore, Garchomp (like everyone) had counters. He was Ice Shard weak, often locked into Outrage, outsped by the Latis, and was troubled by Skarm, Bronzong, and balloon steels. But he went. Yeah, maybe I have the wrong idea about broken vs. breaking the metagame, but in the end it's all about overcentralization. In my opinion, Excadrill does that at least as much as Garchomp did.
Even in this gen, I'll tell you right now that Garchomp without Sand support did not have a striking number of counters. Skarmory is a good check, true, and Porygon2 can now be considered a counter, but all it got was a few more checks; base 102 is still faster than a lot of things and it didn't really get any new counters. What really pushed it over the edge this time around, though, was that even checks weren't safe with that 20% evasion rate factoring at the worst of times and costing games. And when you get sets like Sub/SD that can force it into an even safer position to sweep, most of the voting populace agreed that its time was up.
Thundurus is in a similar position atm. Sp. Def Quagsire is being toted as the #1 counter to Thundurus the game, and yet still, no one is using it. The reason for this is obvious: Specially Defensive Quagsire sucks. Most of the tier's premier special attackers can still 2HKO it easily, and it loses out on its ability to counter physical threats just to cover Thundurus. No thanks.
Even if it doesn't seem like it should be broken to some, there's no denying that Thundurus is just a very hard Pokemon to deal with in general, and a lot of the Pokemon that supposedly 'handle it' can be screwed over with minimal prediction from any one of its standard sets.