No, it really isn't overcentralizing. No more than any other ridiculously powerful wallbreaker, at least. Charizard Y may be able to 2HKO nearly everything and may have few solid counters, but so do a lot of other Pokemon. Charizard Y is not just something you can slap on a team and expect it to immediately break the game in half. You have to be very diligent with your Defog/Rapid Spin support to keep it healthy, even moreso than Charizard X since it loses twice the health to Stealth Rock every time it switches in after the Mega evolution has taken place. This may not be a problem for some Stealth Rock-weak Pokemon, but for a wallbreaker like Charizard Y that often switches in and out to do its job, it's a lot more of a burden. It relies on Focus Blast to beat a lot of checks, and while it may be enough most of the time, it still leaves Charizard Y with about a 1/3 chance to screw up and get killed in return. Charizard X doesn't have that problem since its most common offensive moves all have 100% accuracy.
It often struggles against defensive teams because Chansey/Blissey are so common on them, and each shuts it down (outside of Flare Blitz, which is pretty suicidal in general and doesn't actually do well against Chansey). After it has Mega evolved already, specially defensive Hippowdon (another commonplace on stall and Sand-based teams) walls it decently enough. Bulkier variants of Charizard X can take it on easily and even switch in completely safely if Stealth Rock is off the field (and even if it isn't, Focus Blast needs to hit twice to 2HKO after SR). Goodra is hardly tickled by Charizard Y, even the occasional Dragon Pulse (which doesn't even 3HKO), and it effortlessly 2HKOs back with Thunderbolt (and has a good shot at 2HKOing with Draco Meteor). Latias and Latios are very common Defoggers at the moment, and either can switch in and threaten Charizard Y with Thunderbolt or STAB Draco Meteor. Even 4/0 Latias can't even be 2HKOed outside of Dragon Pulse if it has Roost, while Latios can still take a Fire Blast pretty easily and hit even harder than Latias. Both outspeed, which makes Charizard Y's job a lot harder. In fact, its speed is one of the biggest pressures on it when facing offensive teams in general. Most offensive teams are filled to the brim with Pokemon like Garchomp, Keldeo, Talonflame, Mega Pinsir, Terrakion, Deoxys-S, Landorus, Thundurus, Latios, and a myriad of slower Choice Scarf users that can outspeed it and deal heavy damage to it or outright KO. It might be able to 1-2HKO nearly everything on an average offensive team, but when it's facing Stealth Rock and constant offensive pressure, it's not going to be breaking them down very easily. Let's also not forget how much more insanely tame Charizard Y becomes once Sun runs out (which happens pretty often, especially if you have to switch it out and then back in again before the previous Sun timer ends). Charizard Y has it share of checks and even a few real counters just like so many other Pokemon do, and it by itself is certainly not overcentralizing.
By the way, don't use Earthquake on Charizard Y. It doesn't really help with much. Offensive Heatran is hit harder by Focus Blast anyway, and specially defensive variants are 2HKOed regardless. It's a safer option, but that's about it. Besides, it's not like defensive Heatran does much in return anyway. Generally, the worst thing it can do is poison you with Toxic or hit you with Ancient Power (which only 2HKOs), neither of which are super common moves on Heatran. There are those occasional defensive Heatran that run Stone Edge, which I've seen a few times among tournament players, but those are far and few between. You'd be far better off running Roost to let Charizard Y recover Stealth Rock damage whenever it gets a chance, maybe switch into a few things more easily with its solid special bulk and resistances, and just stay alive in general. You can even stall out the occasional Ancient Power Heatran in case Focus Blast misses and you need to recover from that. You could use Dragon Pulse as well to hit random Dragons harder. Either would be better than Earthquake.
Of course, this isn't a Charizard Y thread and thus this may be a little off topic, but no, I don't think it's overcentralizing. It's very good and extremely powerful in its own right, but I find myself far more worried about Charizard in general with its "Hey, guess what form I am" mind games or other offensive threats altogether than specifically Charizard Y when I'm teambuilding.
EDIT: As the above poster mentioned, I also think that in order to truly be considered "overcentralizing," you'd have to see metagame trends that actually centralize around Charizard-Y. I just don't see that right now; most of the common checks and counters to Charizard Y out there are just good Pokemon in general that would probably get used a lot even if it didn't exist. Now, you might have a point if we started seeing a lot of Moltres usage or something, but that's not the case.