EA/Bioware will do something to further monetize the IP. Unfortunately for us ME fans, I think their options are limited. It is hard to top the epic storyline of the ME trilogy (it's not like they can say "OK we beat back the reapers but now here coms the real AI masters of the universe for you to defeat." They had the same dilemma with Dragon Age. The story for Origins was awesomely epic IMO, which made it fun to play even if the console fighting mechanics were not exactly stellar. But how do you top the blight in terms of epic story? They didn't even try and so we got DAII, which was really not a bad game but the story really didn't compare at all in terms of scale/epicness to Origins. ME will have same problem post-trilogy. There will be games, heck there have even been rumors of a ME MMORPG (which I will NEVER play if that happens). But the story will never match the ME trilogy. This is one prediction I would love to get wrong.
There needs to be a prequel trilogy. I know those two words have a hugely negative connotation for us familiar with Star Wars, but you simply can't put anything after what is being touted as the epic conclusion. Show us the Rachni Wars, Krogan Rebellions, geth/quarian Morning War, and First Contact War. Then we'll talk stuff post-ME3.
Do you mean at the Conclusion of the game? Well in that case it's either being paraded in front of the galaxy as the Great One. Or being raped by the Reapers i think it depend's on your choices in the last 2 games
There will be more games about Mass Effect universe, only without Shepard. Otherwise, if you mean what happens after ME3 is released... 21.12.12 is the end of the world, right? :P