The problem is the balance between finding out where innovations is due and where it's stifling. With the cover system you mentioned, for instance, why wouldn't you allow cover in your game? Because without cover the game plays completely differently. Think of how Duke Nukem 3D or Serious Sam would be like with a cover system - they wouldn't be the same game. So, taking this as an example, a belief that there's no need to 'innovate' the cover system begets several games that don't understand why it exists (to create a slower experience in which precise rather than frantic combat takes place) and we end up with games like GTAIV, in which you spend hours ducking behind a dumpster waiting for a bunch of guys to peek out of a column. It's realistic, sure, that's probably how real life thug firefights go down, but it's not fun at all. Meanwhile, Saint's Row 2 knows what it's doing and presents no cover system, instead opting to let you prevail over your enemies by giving you weapons that in the real world are only found attached to airplanes. I'm not saying frantic is better than precise, but I'm saying SR2 is better at being frantic than GTAIV is at being precise. There are many shooting games that fell into this trap and are too precise to be fun.
A good designer must examine all gameplay clichés and figure out what they exist for and where he can change, come up with something new or even bring back something old. That Rifts game looks like it's headed well, but since I don't care about MMORPGs I have no opinion about it.