Fischer is actually a pretty interesting character. First of all, the whole movie revolves around his reconciliation with his father and the realization of his own identity as existing separate from his father's legacy. When we first see him, Fischer is in the room with a dying and irascible Fischer Senior who symbolically breaks a picture of Fischer and a pinwheel, so yeah, he's having a bit of a tough time. His father is dying, his father doesn't care about him, and he's inheriting a massive energy corporation.
It's nice that the team decided on such a happy ending to the dream, because when Fischer finally sees projection father, it's a happy moment for father, son, and extractors alike. Except that… it's a bit more complicated. Sure, it's happy for the extractors because they succeeded, but what does their success mean to us, the audience? What if Saito is just trying to make a power play in the energy business and is ousting a competitor? Is there really any way we can know for sure that Saito is just a good guy trying to do a solid for consumers?
Also, we have to remember that not only is his father a projection, but Fischer himself is, dreaming. There was never any reconciliation at all outside of the dream created to simulate reconciliation in order to produce inception. It's just an elaborate scheme and Fischer is the target, or as they say in heist movies, the mark.
Feel as happy for Fischer as you want—maybe the inception will be a good thing for him and Saito in the long run. Keep in mind, though, that all of this happened within Fischer's mind and, unless he pulls a Mal, Fischer knows what's real and what isn't (by which we mean his dad is still a jerk).