You're stretching it a bit by calling Other M and the two Resident Evil games "shooters". Although, you may be right, and Resident Evil may be part of the problem. It used to be a survival horror/action game. It's a shame that now it is lost amongst that crowd of third person shooters. (Other M is a platformer, all day long, for me)
I remember the days of old where people used to argue that Metroid Prime was a third person adventure rather than shooter. Yes, you do "shoot things" but it was almost a category of its own.
Personally, the big problem I have is to do with setting. Notably, the Call of Duty and Medal of Honour games are guilty of reusing the same setting over and over again. I personally dislike that, and it's games such as those which give the entire genre a bad name. In addition to that, the "space" shooter genre is being a bit saturated. Aliens: Colonial Marines was intended to be the King of this genre, the story mode looked excellent...alas, it wasn't meant to be.
What I don't really like about certain series' is that they are almost being "tech fests", where it becomes a case of how "impressive" a game can look or what it can do, rather than actually being fun or exciting to play in itself. I've mentioned this before, but TimeSplitters 2 nailed this for me. It had reems of content, looked quite nice with its graphic style, had a good multiplayer, map maker, etc. But, it just didn't click for me, it didn't have a soul like Goldeneye had in the past.
Red Steel 2 was interesting in that it had a nice art style and great sword controls. The mission structure wasn't right, though, which fundamentally let the rest of the game down. It seems hard for shooters to get everything right, and those that do are the rare awesome quality ones.