I'll try to explain why! If somebody else could correct me if I'm wrong that'd be awesome~.
The two decks out there that are top contenders -
ZekEels and
CMT - are able to include Mewtwo into their decks with no issue whatsoever. Heck, CMT was basically designed purely with Mewtwo in mind. With the Eelektrik engine for Lightning energy, and the Celebi / Tornadus engine for Grass, you are able to start hitting fast and consistently. Mewtwo has 170 HP - meaning that it is almost guaranteed to take 2+ prizes against most of the decks listed in the
Metagame Deck Center. Let's not even get into Tier 3 decks! Mewtwo is a Basic, giving you an extra option to search via Pokemon Collector and a few Pokemon abilities.
You may think that I just described the motto of all EX cards - It's because I did. Basics with high HP, and attacks that do high amounts of damage from the gate. Well, not from the gate. Only Mewtwo starts attacking on turn 1, and that's what makes him so powerful!
He fits into any deck - all it takes is one Double Colorless to start hitting for 40+ damage. His damage will rise considerably if you try to attack him back, since the only cards that do enough damage to threaten his prize ratio will most likely be one-shot or blocked by the other Pokemon that Mewtwo gets together with. This instantly takes so many cards and strategies out of the equation that it's not even funny.
When taking all this into account, you might start to see why Mewtwo is so relevant in this format. The BDIF currently, ZekEels (at least, in my opinion~), already had an amazing engine and set of cards that probably would have made the deck a top deck in the first place. When you add a Basic that can almost always win the prize trade against non-EX cards, it just adds to the solidity of the deck. Once you have a clear sight of the 1-3 decks that abuse the fact that they smash the majority of Tier 2+ decks, you have to start coming up with strategies to keep other decks relevant. And sadly, the best counter thus far to Mewtwo is another Mewtwo.
Mewtwo isn't required to have fun or to have a good, thought out match. But, if you want to win tournaments, and not just play with friends that have a truce, you'll have to find some way to go up against it until Dark Explorers and the un-named Dragon Blade and Dragon Blast english expansions come out.
TL;DR: EX cards are good. Mewtwo is better than most. It his hard, fast, and consistently. It alone smashes a lot of Tier 2+ decks. It fits easily into decks that are already good, giving them that more of an edge against every other deck. Thus,
near everyone needs to run it, or else their deck will fall flat on it's face if the goal is to beat the best decks at tournaments right now. And because they are all trying to beat the best with Mewtwo as one of their tools, you need to account for almost all decks having Mewtwo as well, or else they'll use it on you!