Still developed by Ed Boon and his team at Netherealm Games

Games that come to mind all had financial backing of Square-Enix

Tomb Raider (Crystal Dynamics) - Taken over from Eidos Interactive
Deus Ex - Human Revolution - Taken over by Eidos Montreal (very different team than the Warren Spector originals)
Sleeping Dogs - Taken over by United Front Games (converted from unreleased True Crime - Hong Kong)
Hitman Absolution - IO Interactive - Taken over from Eidos Interactive

It is rare but it happens.

PS - A Thief reboot also funded by Square-Enix is on the way out I think as close as February.

Red Dead series being picked up by Rockstar from Capcom? I'm not sure it counts as Rockstar picked up the first one before release but it was mainly developed by Capcom and finished off by Rockstar.

I don't really see a comparison with Gears of War...

Microsoft had exclusive rights and contracted Epic to make the first four games.

Technically, the IP is not changing hands as MS published all four of the first games.

All that is happening is that MS is taking on the development as well.

You realise That Eidos was a publisher right? and that Square Enix aquired yhe whole thing developers and all. And was renamed SE Europe so doesn't really count in the spirit of the OP as the IPs never really changed hands the entire company that already owned them did.

Deus Ex is debatabletho it is better than the Invisible war train wreck.

Tomb Raider switched developers from Core design to Crystal Dynamics back in 2006 with Legend still published and owned by Eidos at the time.

Sleeping Dogs was always developed by United Front Games even back before it was a true Crime game (it was Called Black lotus and had a female lead) and the entire almost complete game was sold not including the IP. So doesn't count for the topic.

IO Interactive was the developer of all the Hitman games.

I disagree. A spiritual successor/predecessor to a game is still a successor/predecessor in my opinion, even if the original IP can't be used.

Well, I'm just going by the technical definition of intellectual property. If that's how you feel, it's not a problem or anything.

If you want to count Banjo Kazooie, Nuts and Bolts was far better than Banjo Tooie.

Some people say Halo 4 was the best one. I disagree, but the quality was still extremely high so the game remained just as good as it was before.

I welcome the criticism or this. I will defend it with all I know.

Halo.

Under MS's full control, Halo 4 looked better graphically, it tied itself better to the extended universe (novels), the cutscenes were CGI and not in-game, and the lore was expanded while making the story more emotional then Bungie ever did (with Chief and Cortana namely).

About the only, and major granted, complaint was the MP. On day 1 it lacked the modes and balance issues that Bungie excelled at. Now, Halo 4 is how it should be, but many view it as too little too late. 343 has acknowledged this and staffed up considerably and listened to feedback, so MP modes, balancing, and community features will definitely get more attention in Halo 5. Firefight will hopefully come back.

But it was the campaign where 343 excelled in ways Bungie never did. People forget that it was under Bungies direction that retconned The Fall o Reach, which is regarded by most diehard fans as the best Halo novel. 343 will never have such a disregard for the lore.