Well, I will say that I think the term "shooter" has become sort of obselete and is simply being used due to the amount of time it's been in circulation. It would be more accurate to label these games "combat simulators".
That said, close quarters combat is a big deal especially when you see engagements at that range regularly. It depends on the exact circumstances, in a lot of cases if you have the drop on someone and they have a gun, even a shotgun, it's relatively easy to force that weapon out of line and stab them. It comes down to who is reacting to who as much as anything.
I do not consider the dominance of melee weapons in such circumstances to be that big a deal, although I don't play this genere too often. Generally speaking if you keep dying to things like this, you should probably avoid letting people get that close.
Generally speaking, the ideal evolution of the system would be to put more effort into close quarters combat systems and how hand to hand range combat works. Of course this would both make the game more complicated, which would probably be an anathema to those who play these games for their simplicity, and would of course probably be part of a package focusing more on realism in terms of recoil and actual firearms usage. Looking at games like "S.T.A.L.K.E.R." (which I enjoy quite a bit) a lot of the casual "I can't deal with anything statistical or complex" shooter fans were turned off due to the fact that shooting just wasn't as easy as it was in other "FPS" type games. Trying to shoot a moving target at a hundred yards with an AK-47 or the equivilent not exactly being a joy, where the equivilent is comparitively easier in say "Modern Warfare 2" where for all pretensions of realism they modified things so even a 10 year old could feel like an elite member of the special forces.
With games set in the far future things become touchier, your using things that don't exist (and probably never will) like powered armor and battle suits. People aren't going to lug around these shield generators and strap several hundred pounds of mechanized metal to their body if they aren't effective. If firearms were unusually effective against such armor then nobody would use it and we'd see an evolution like we did when firearms first hit the battlefield and everyone put their plate mail away and just carried guns.
A number of science fiction series have addressed guns being effective and used, while melee can be more so (with people charging through fire to engage in hand to hand). Things like there is only so much punch a bullet is going to pack, even coming down an electromagnetic rail, yet someone using a melee weapon perhaps with a seperate power source, backed by a ton of dedicate servo motors is going to do a lot more to get through a metal plate. Sort of like how (for real) you can bounce bullets off say the hood of a car, but then take a decently thick blade and cut a slash right through it. Not to mention that it's easier to hit something like a joint with a melee weapon especially if the other guy doesn't have one and your as fast as he is, than to do it with a gun at a distance (though by no means is it ever going to be simple).
The point CAN be argued, but if you want combat to flow well, melee is something that shouldn't be overlooked, and chances are if someone with an appropriate melee weapon ready is attacking you (even with a shotgun) before you can react, you should be dead. Realisitcally I guess a guy would say grab the barrel and push it away as he attacks, but there are limits on animations and how well they flow even in PVP.
As one final point, I haven't played the new Transformers game (budget bin material for me) but I'll point out that in that setting melee SHOULD be really powerful because that's how a lot of key battles are resolved. Sure the robots carry guns, but you don't see many of them getting blown to pieces with a couple of shots. On the other hand in the comics and such they do tend to rip each other apart when it comes to swords and blades (probably using the same logic as with the armor above). This is one bit Michael Bay more or less got right.
As a final note, I will say that I think that if "shooters" ever evolve into a "smarter" gaming genere, games are probably going to be built from melee on up. I look at games like "Zeno Clash" as an example of what first person action based melee can be like. The trick is going to be to balance something like that with shooter mechanics as well. If someone comes around the corner in front of you, but still surprises you, carrying a knife, it will turn into a melee battle you might recover from (think Jason Bourne or whatever). Right now though, the "one button kill" is a fair way of doing something if he presses first, not to mention there should be some payoff to getting into position to do that. I mean the guy probaly isn't moving any faster than you are, and if he's killing you with knives that means you need to be more careful.
