Otherwise you're saying it's ok for a Wizard to take an ordinary sword and infusin it with magical energy to make it +2 Flaming, but its is not ok for him to pick up a +2 Flaming Battle Axe and suck the magic out of the item entirely then infusing a longsword with it?
That's more or less how I feel, actually. To me, magic is not something you just pour into an item; it's integral to the item itself. You don't forge a normal sword and then turn it magic. The enchantment takes place as part of the forging, and alters the properties of the sword.
To put it in a real-world context, say you have a Damascus steel sword and a crude iron battle-axe. You can't suck the Damascus out of the sword and pour it into the battle-axe. I look on magical properties as being the same kind of thing.
What I'm planning to do instead is give PCs books of magical lore and special ritual components that enable them to create magic items with particular abilities - for example, a lore-book explaining how to make a Thundering weapon, and enough dedicated components to create one such weapon. That allows them to make weapons that fit their needs, without grinding my DM gears. (It also gives me a nice little quest hook, if the lore-book calls for something like dragon blood in addition to the other components...)
Also, in my games, "named" magic items tend to level up with the character - one of my PCs has a frost weapon whose numeric bonus scales with the level of the wielder. That way he doesn't have to get rid of his family's ancestral sword just because he's outgrown it, and I don't have to hand out an endless series of magic longswords to keep him adequately armed.
Back on topic: Extra damage is good. Superior weapon proficiency gives you ~1 hp extra damage per attack. However, so does the feat Weapon Focus. So if you don't want to specialize in a single weapon, take a weapon group instead.
You're missing one important element, though. Weapon Focus gives you +1 per attack. Superior Weapon Proficiency gives you (on average) +1
per weapon die. Your basic attacks for 1[W] get +1 damage either way; but an encounter power that does 3[W] damage still only gets +1 from Weapon Focus, but +3 from Superior Weapon Proficiency. Thus, at Heroic tier, SWP is the better feat.
Of course, Weapon Focus scales with tier, which makes it less clear-cut as you advance.