Of course they will. While Microsoft owns much, the Indy market still produces products for niche groups that Microsoft (and other big companies) will never touch.
Niche products for niche markets, of course, sell less than big titles for "everybody", so they have to be made with lower costs in other to be sustainable, if not profitable. Big companies have to maintain "Brand Integrity", so all they make need to look and feel Triple-A. This makes costs go super high, then it needs to be either super monetized or as appealing as possible.
There is no space for Paper Checking simulators, Polemic stories, Heavy War stories, depressing games, and so on. Things need to be for many people, or for people who have no economic constraints.