Ubers was intially a banlist but has evolved because there is a growing playerbase. Now that it has become more popular it's considered a tier and like all other tiers the players want to create a competitive and mostly balanced metagame. If there's a Pokemon or ability that the players feel is broken or overpowered then they should have the right to call for a ban. Why not? I don't understand the "Nothing should ever be banned from Ubers" view or the "Natural way" as you described it. Using a Mega Gengar to check another Mega Gengar is not fun. If that's how you want to play then by all means play custom games. A majority of the people who play Ubers want a tier that's enjoyable and competitive at the same time.If Mega Gengar is such a big threat, shouldn't you be constructing your team accordingly and not creating any major weaknesses to it, just as you would for any other threat like Kyogre, Xern, etc? Yes, Mega Gengar is arguably slightly different in that it can trap things, but for the most part, it's still only as good as what it can trap. If being able to trap and remove things is such a successful strategy, you should be doing it too, so then both you and your opponent will have to play with this in mind and therefore it will still come down to who uses their resources better and makes the better predictions (this game is naturally quite heavily luck based, so take that statement with a grain of salt). We've already established that centralization is not a criterion for banning something, so if you need to use Mega Gengar in order to have a better chance to win, isn't the case then "so be it"? It's like how >50% of teams use Xern and how the game frequently comes down to who finds the best opportunity to set up with it and sweep first.
The team-building aspect of it should also balance out; you can build around not being weak to Gengar and being slightly worse against other threats because of it, or you can you build your team to be better against other threats but weak to Gengar. Then, when it comes to your opponents choice in this regard, if you happen to come across a team who hasn't built their team around not being weak to mega gengar in hopes of being stronger against those that don't have it, you can simply remedy this issue by using one on your own team to punish that 'greedy' choice. If everyone does that, Mega Gengar will be centralizing, but not problematic, just as any other premier threat is.
Mega Gengar also has issues associated with it which aren't favorable to the user that prevent it from being some 'unstoppable force', such as having pretty awful bulk which restricts its switch-in opportunities, having to stay in for a turn first before it can actually trap things to begin with, and having a Pursuit weakness. These aren't exactly glaring issues, but they certainly make gengar manageable and tolerable.
So my current stance on the matter is that Mega Gengar is centralizing but not uncompetitive, and calling Gothitelle a problem in Ubers is, frankly, a joke. If we start banning more and more things like Shadow Tag in Ubers, we're gunna need a new tier above Ubers that has no clauses at all so that players who actually want to be able to play the game as close to the natural game as possible without all these recent cries of uncompetitive mumbo-jumbo, can do so.