It's obviously bad if players can use their spells to gain some extra power. Having spells and knowing how to use them effectively should make no difference in a character's power.
I tihnk the real problem isn't so much with greater magic weapon as it is with the lack of other spells. If there was a spell similar to GMW that gave effective enhancement bonuses for special abilities and overwrote GMW, then more people would want vanilla +X weapons so they could use Greater Weapon Enhancement or something.
Spells <> Magic Items
A character can use spells to duplicate effects on magic items or use magic items to duplicate the effects of spells. Most magic item seem to follow this rule. Boots of Speed = Haste. In many cases, the magic items are much better of of their durations. However, they're roughly equivalent.
However, in the case of magic weapons, spells that give special abilities don't scale as well as GMW, and thus are less efficient. Therefore, casters prefer using GMW to boost others' weapons. Next, the fighter types who use the weapons will tend to want weapons with lots of special abilities since GMW seems so good and everyone uses it. After all, there's little point in going to great lengths to aquire a +3 weapon if the GMW is equal or better.
However, spell equal to GMW that gave abilities would mean that casters could use either spell to great effect. Then permanent enchantments would reflect either whatever spell the creator didn't like using, or what the recipient of the weapon thinks is necessary for bare minimum performance. This bare minimum preference will vary more depending on style. Rapier weilders will almost certainly want automatic Keen weapons, since they benefit most from it, dual weilders might want elemental damage, and surestrike on the off hand weapon, archers will still get magic bows and hope for spells on arrows because arrows are too expensive - by the time they can afford them, they'll probably have 3 shots per round and thus eat a stack of 50 enchanted arrows in less than 20 combat rounds; too wasteful, especially for high end weapon - tanks will probably go for extra plusses so they can hit every attack and gain extra damage with power attack if need be.