Here's how the whole "Ogre Battle history" thing works, as far as I know.
Ogre Battle is/was made by Quest, and mostly (at first) published in Japan by Enix. Quest wasn't a "partner" of Enix, like Armor Project or Chun Soft or Tri Ace, they just got their games published by Enix.
The first Ogre Battle on the Super Famicom got released in America by Enix of America.
Enix didn't release Tactics Ogre (the second game) on the SNES in America, because those jerks at Enix of Japan came to the conclusion that any money invested in Enix of America (although profitable) would make more money if it was invested in developing more games JUST for Japan, therefore it was "wasted" on us, so they shut down Enix of America.
Then on the PlayStation, Square needed more employees, so they bought half of Quest's original "Ogre Battle Team", including Yasumi Matsuno, the "team leader". They eventually made Final Fantasy Tactics, and Vagrant Story.
Quest used their "half-sized Ogre Battle Team" to port the two Ogre Battle games to the PlayStation, and used the money to hire more employees and get back up to full strength.
Atlus decided to publish the two PSX games in America (Enix of America was still out of the picture).
Then Quest made Ogre Battle 64 on the N64, but Enix (in Japan) didn't want to make any N64 games, so they refused to publish the game. Nintendo (NCL) stepped up and published the game in Japan.
Atlus and NOA apparently both wanted to publish Ogre Battle 64 in America, but Quest decided to give Atlus the nod, and put Atlus "in charge of the Ogre Battle series in America".
Atlus published Ogre Battle 64, and the side-story "Tactics Ogre Gaiden" on the GBA (Atlus skipped releasing the earlier "Ogre Battle Gaiden" in America on the Neo Geo Pocket, for obvious reasons).
Then Nintendo got back together with Square, and Square was impressed with Tactics Ogre Gaiden, so they bought the entire "new Ogre Battle Team" away from Quest, and had them make Final Fantasy Tactics Advance for the GBA, under the direction of Yasumi Matsuno.
A few weeks later, Quest gave up on trying to stay in the videogame industry, so they sold the rights to Ogre Battle (and anything else they had) to Square, and went off to invest their money in some other industry.
I haven't heard anything about the Ogre Battle Team (not an official name anymore) working on anything else at Square, but they may have been involved in FF1&2 for the GBA, or they might be helping Yasumi Matsumo with Final Fantasy XII.
Yasumi Matsuno has said in some interviews that he'd really like to be in charge of an Ogre Battle game again, now that Square owns the rights to it, but that he's completely swamped with working on FFXII, so he can't think about any other projects right now.
Since Quest sold the Ogre Battle series to Square, Atlus has apparently let go of their claim on the American rights to the series (at least, according to the US Patent Office website, they have), so any future Ogre Battle games will most likely get published in America by Square-Enix.