There are three problems with superior weapons and implements.
Combining weapon types or properties is just hazardous for balance. At one point spears were low proficiency and low damage, so the feat support they got, was reasonable. That support turns into power creep with weapons like Gouge that combine spear and axe with big damage, particularly after considering powers, enchantments, feats, and to top it all off, classes who primarily make basic attacks, combined with some of their feat support.
The second problem is proficiency bonus. 1-5 extra damage for 1[W] through 5[W] powers isn't as big a deal as not missing with Storm of Blades, or landing all your Rain of Blows attacks when you're trying to take something out. An invoker wants to eek out every bonus to hit, if he wants to land that Silent Malediction, so as a Human Invoker, I feel just about obligated to start with staff expertise and accurate staff. A reach spear fighter would feel foolish not picking up great spear. I don't see anyone using longspear as their primary weapon, for any length of their career.
The third problem is psychological appeal. Player A warhammer sees player B with Craghammer rerolling his 1's and 2's and every damage roll, and every time player A rolls a 1 or 2, players B says, you could be rerolling that. Peer pressure, player B picks up Craghammer. Hearing "My weapon is bigger than yours" is at times more effective than any mathematical formula.
Should they stay or should they go? I think they should stay. There are too many, what I think are mistakes, with military weapons. A control focused fighter using a polearm is stuck with a +2 proficiency weapon, when his function is highly reliant upon hitting. Superior weapons and implements just make you feel more competent, and competency is good for any character. I do think the combined weapon type issue needs some monitoring, to see where there may be abuse.
Is it good for superior weapons and implements to cost a feat? Well, I have no answer for that currently, until they separate design spaces for feats. For each player group, game, or DM, it will vary. In my paragon game, only 2 players out of 6 use a superior weapon or implement, the rest don't seem interested in bigger damage, or +1 to hit, or other benefits of a superior weapon. So I don't give the feat for free. But if a game I'm running has a bunch of optimizers who all want to pick up a superior weapon or implement, I'd have no qualms about handing it out for free.