I do miss having to have a seperate melee weapon in FPS games because to a certain extent it does make shooting at close range somewhat pointless (when you can have an instantly lethal, extremely accurate, requires no ammo and has a suprising range for a knife).
My issue with knifing in games is not tied to realism, it's tied to the fact that it's often a broken game mechanic.
Why bother lining up a shotgun blast when you can just warp a few feet and shiv the bastard insted? The recent trend in melee buttons usally ends up becoming what I call the 'save me button', a get out of jail free card for people who panic when someone comes within their comfort zone (why bother with close range shootingwhen you can immediately remove a troublesome player by stabbing the air next to them, and then resume firing almost immediately?).
Melee weapons used to have their high damage and speed come at the price of range and long range vulnerability (they were weapons of oppertunity at best and emergancy weapons at worst), as it stands at the moment someone can snipe someone, knife you and then proceed to snipe someone else in the very next instant with no pause in between.
If you are gonna have melee as an attack usable with every weapon then I think that the Gears of War way of doing it was the best, that being, (namely with the chainsaw) getting shot will bar you from being able to melee for a brief period of time (this would keep melee as a usable option if done right but prevent people from simply using berserker tactics and witching classes).