I am pretty disappointed they changed the multiplayer game of Spies vs. Mercs. That mode was a lot of fun and one of the main selling points for me after the SP was finished.
 
Does anyone know why they may have gotten rid of this mode?

Splinter Cell Chaos Theory has the best multiplayer ever. I'm really sad it didn't make it to Conviction, and while I understand the reasons they gave for not bringing over that multiplayer, I would have accepted the exact same mode with new maps and gadgets and such. Sad face for the lack of no Spies Vs Mercs.

Probably because the team wanted to make a new game with new multiplayer, and not use something they've already done before.

Co-op has always been the highlight of the online Splinter Cell experience. With a drastic overhaul of features, dodging the multiplayer this time around is incredibly rational. I think people expect too much from developers. 
 
I mean, Ubisoft entirely reformatted one of their biggest franchises. Hell, they redid the entire approach to stealth. And what's the end product? A fantastic singleplayer experience with many varied locations, tons of variety, incredibly cinematic presentations, and a very robust and replayable co-op. 
 
Want to get into DLC? You're getting free weekly content. And there's talk of a potential DLC multiplayer mode (spies vs. mercs) coming--if they come up with something decent.