Ever since Mojang grew into a fully-fledged company (e.g. once Notch hired some help) development has been surprisngly slow and hobbled. With the Microsoft acquisition, we may actually see faster and more efficient development. This could also be a bad thing though. Will Mojang go the way of Rare, a previous Microsoft acquisition now devoid of its original charm and flare?
Minecraft is currently the 3rd best-selling game of all time, selling over 50 million copies. Those 50 million in sales have already happened. While more sales are still occurring, the number to come is probably less than what has occurred. When I bought a copy of Minecraft in 2010 the license was "free updates forever" (if I remember correctly), at least until the full version was released.
Mojang has continued the tradition of free updates since the game exited "Beta" in 2011. I can't imagine players would be thrilled to have to start paying for the same sort of updates they've been getting for free for 3 years.
So if Microsoft wants to earn some dividends on the ongoing development of the game itself, they're going to need to release a huge update: Probably a sequel.
There's a lot of reasons to do a sequel beyond the financial benefits though:
Escape from Java
Java is not very performant. At all. While it certainly empowers cross-platform development to an extent, it is not necessarily the ideal language for the project.
Microsoft would definitely be motivated to rework the project in C++, since C++ is one of the languages Microsoft pushes. It also helps that Minecraft Pocket Edition is already written in C++.
A pretty significant limitation of the current incarnation of Minecraft has been its chunk file format. While this has been gradually improved over the years the game is still limited vertically because the chunk format goes from bedrock to sky ceiling. It has stayed this way because re-writing the format is incredibly complicated and requires reworking a whole lot of the code.
Rewriting the whole thing from scratch could enable the team to rebuild Minecraft on a better foundation.
I for one am optimistic (cautiously so) that this acquisition could potentially bring about everything the community asked for and then some: Modding, better performance, and more reliability. Or not. Fingers crossed!