It's pretty much undisputed. Magic: the Gathering is the #1 TCG in both Sales and OP, and there is really no other TCG out there that can come close to that. Everybody else is pretty much fighting for 2nd place.
Pokemon wins the sales over YGO because of all the kiddies who get Mommy or Daddy to buy them a pack each time they go out shopping. YGO sales are pretty much tied directly into OP, while Pokemon sales are tied into the strength of the franchise. Currently, Pokemon is one of the strongest video game franchises in the world, and the only (primarily) videogame franchise to launch multiple successful offspring into different forms of media (TV and TCG being prominent, but figurines and plushies are also strong).
YGO probably has the stronger and larger OP because the game pretty much requires a strong OP in order to sustain sales. Unlike Pokemon, YGO was a TCG first and foremost. If the TCG dies, the rest of the franchise dies along with it. So Konami has to make the OP as strong as possible. The same cannot be said of Pokemon. If the TCG goes belly-up, there's still a strong following of both the VG and anime. The VG is the deepest RPG game currently on the market. The anime is very popular amongst the 6-14 age group, both here and abroad.
This announcement of Konami taking over the entire YGO reins isn't shocking. They're trying to pull a Pokemon by cutting out the middle man and making a stronger game for it. The problem is that they tried it in the same way the French decided to do their revolution copying the Americans. Too much, and too fast. Pokemon waited for their licensing contract to expire with WOTC before taking over, so there were few hard feelings amongst the players, and the licensee (WOTC) wasn't as ticked off by the entire ordeal. UDE still has a year left on their licensing contract, but Konami is pulling the rug out immediately, leaving nothing but a sour taste in pretty much everybody's mouth.
My prediction is that YGO will decline for at least 6 months (if the recession continues, probably more) because of this sour taste. What happens after that is entirely up to Konami and how they handle being in charge over those 6 months. If they provide less or even equal support as UDE, then the players that left will not come back, and the player base will be smaller. They'll have to do something more than UDE in order to maintain their (very strong) organized player base.