Great answer by Aydenbro0987, but I wanted to add something to it.
I'll use three main sources in this answer;
These are very much reliable sources that you can trust (do I need to say this..).
Without any further ado, let's get to the answer.
In late 2014, loads of questions were raised. The government (supposedly Smogon's Staff) were aware of the furore of the Uber players. The meta was in a state of turmoil. The Ubers players were leaving the tier to play other tiers. The main reason behind this was the uncompetitiveness of the tier. Where did this uncompetitiveness come from? Exactly what happened? And why did the players consider leaving the tier rather than going to McDonald's and eating a McEgg? To these inquisitive and puzzling questions, we'll have an answer here. Get ready to travel back in time....
Ubers was quite a healthy metagame in lots of ways. Darkrai couldn't put a whole team to sleep and watch them crumble, for the Sleep Clause existed. Taking six Arceus and having fun with Toxic and random Calm Mind users was also a no-no, as the Species Clause existed.
But then came a fresh new wave which took advantage of these clauses which were there to make the tier better.
This fresh wave was Mega Rayquaza.
With sky-high and well-distributed stats, a stellar movepool, rivalled only by the Movepool Gods Mew and Arceus, and (one of the best points, this one) the ability to Mega Evolve without a Mega Stone, Rayquaza-Mega soon became the most desired Pokémon of the Ubers metagame.
When Game Freak first released Omega Ruby and Alpha Sapphire, the public was amazed. Rayquaza Mega Evolved with a move, Dragon Ascent, meaning it could hold any item. With ridiculous stats and a powerful STAB move, as well as one of the best offensive types in the game, Mega Rayquaza became an overcentralizing force in Ubers. Using a different Mega outside of Rayquaza was unthinkable, and the opportunity cost of not using it was tremendous. With a single Dragon Dance, base 180 offensive stats, and a base 115 Speed, Mega Rayquaza could outspeed a majority of the tier while literally 2HKOing everything with Life Orb Dragon Ascent, outside of obscure checks such as Counter Skarmory and Shuca Berry Rhyperior. Klefki and Sableye were not even reliable ways to check it because it could run a Lum Berry as well.
Mega Rayquaza's ability, Delta Stream, made setting up even easier. Thanks to Delta Stream, Mega Rayquaza could set up on Primal Groudon, another metagame defining force, and had a resistance to Electric, a neutrality to Rock, and a reduced 2x weakness against Ice. All of these combined factors caused Mega Rayquaza to take the ultimate banhammer, completely changing the policy of Ubers.
It's usage was compared to Xerneas and Dakrai, which were the unarguably, a few of the best Pokémon in the whole tier. It was unreasonably centralizing. Think 70%+ usage. Even Xerneas was ~45% usage. It was almost zero fun to watch an Ubers match with a Mega Rayquaza. Matches then became to be dependant on who Mega Evolved their Rayquaza first. This meant that matches became boring as hell.
It is no fun to play or watch matches with this Pokemon/ability/etc (henceforth just Pokemon) allowed. Having this Pokemon in Ubers makes me want to play some other meta. I would be bored as **** to watch a match with this Pokemon allowed. This is a subjective criterion, but an important one I think: if everyone hates Ubers, then why have it? It is our obligation in such a case to try to fix it.
Chaos put it correctly, Ubers became one of the least played tier.
Mega Rayquaza's simply unbelievable base 180 offensive stats immediately come to mind. It has no problem using them effectively with its wide offensive movepool, which lets it lure in and smash some of its would-be checks, and access to setup moves in Dragon Dance and Swords Dance. Dragon Dance and Extreme Speed help patch up its impressive but not exceptional Speed, which leaves it outsped by threats such as Fairy Arceus, Mewtwo, and Darkrai.
While Mega Rayquaza's bulk isn't particularly noteworthy, it is bolstered by a solid defensive typing in Dragon / Flying and helpful ability in Delta Stream, which halves the damage it takes from Ice-type attacks, removes its weakness to Rock, and turns its neutrality to Electric into a resistance. Notably, Delta Stream lets it survive an Ice Beam from Primal Kyogre, as well as a Life Orb Ice Beam from Mewtwo; Mega Rayquaza can then set up a Dragon Dance and OHKO even Primal Kyogre's most physically bulky set with Dragon Ascent after Stealth Rock damage. This is a feat regular Rayquaza could only dream of.
Mega Rayquaza's ability to hold regular items, in addition to its many other strong traits, gives it an offensive versatility almost unheard of for a Mega Evolution. Lum Berry is the premier option, letting it shake off a turn of status from Pokémon like Klefki and pound them with the appropriate move. It also is a deterrent to many users of status moves, as giving Lum Mega Rayquaza a free turn to use Dragon Dance could result in a sweep. Mega Rayquaza has more room than most Pokémon to run Lum Berry due to its many advantages, including the ability to set up. Life Orb is another viable possibility, giving some extra power and keeping move choice freedom.
These all positive traits just aided Rayquaza-Mega to create history by becoming the first-ever Pokémon to be banned from the ultimate banlist, Ubers.
These are just a few points about why Rayquaza-Mega was deemed too much for Ubers. For more information, please refer to the Sources listed above.
Hope it helped!