I think even 4E has a distinction between halberd and spear and 3E has quite a lot of different weapons which are "a shaft with a blade on the end"
And there are distinctions between magic missiles and other low-level spells that do damage. The presence of these spells doesn't make "magic missile" unworkable as a class of spells that vary by their creator but all have the same abstract mechanical effect, just as "spear" is a class of weapons that vary by their creator but all do the same abstract mechanical die of damage.
We may have a different idea what "creativity" is. Imo, creativity is using what you have for the best effect, not reflavour what you have so it fits the situation better than the standard version.
"Reflavor so it fits the situation better" isn't what I'm talking about. "Reflavor so it fits the
character better" is what I'm talking about. I'm talking about the swamp witch whose magic missiles appear as green, faintly sickly bolts of witchfire every time she casts them, as opposed to the alchemist whose magic missiles appear as shimmering golden bolts of force with alchemical sigils hovering in their center every time he casts them. A character might find an advantage in the right situation (though it's super-rare), but they aren't guaranteed that situation every time. It would be up to the DM to make sure that the situation recurs all the time to grant them a real advantage. (And at that point, the problem becomes minute compared to comparable activities, such as using undead all the time: a real way to hose a 3e rogue, or give the 4e character with lots of radiant damage a serious power-up.)
The thing I'm looking for here is a roleplaying advantage. I find these really important. At its heart, D&D has a lot of silly improbabilities that can knock you out of immersion — it's part of the game's charm, and I love it, but I also value anything that will allow players to focus on what their character sees rather than the rulebooks. I want them to see "orc dragonpriest," not "orc 5th-level cleric, what domains do you think he has?" And I want them to think of each other's characters as "Aaron's giant-blooded mystical librarian," not "Aaron's goliath bard."
And of course, not every reskin is allowable. You can't reskin a magic missile as "A wound opens up on the enemy, and nobody knows where it came from!" You're still a caster, and spellcasting is still noticeable. This is less true of things like 4e monster reskins, but the nature of that particular edition is that the unpredictability of monsters is supposed to be present, and players have plenty of advantages to compensate.
With simple reflavouring you will end up in situations where "my magic missile is better than your magic missile". When you are fine with that ok, but imo this is unfair towards the players. And when you don't want this to happen you limit the players creativity by asking them not to be creative or reduce the flavour by ignoring obvious differences.
Well, I look at it like this. If you reskin, you may limit the players' creativity or reduce the flavor in circumstances where a player would like a reskin that grants them an unfavorable amount of advantage.
If you don't reskin, you limit the players' creativity and reduce the flavor
all the time. The swamp witch and the alchemist have exactly the same flavor to their spells. The death-priest's "cause wounds" just makes sword wounds appear, as does the fire-priest's, although it would be more creative and flavorful if one created wounds that resembled necrosis and the other created wounds that resembled horrible burns.
I'm willing to accept a small chance of "sometimes it might not work as well as a player would like" to in order to get "the players are encouraged to make their characters distinctive and singular with every new power they pick up."
And then is also breaks versimilitude that spells can have vastly different looks, etc. but do 100% the same.
There I don't agree at all, because the game mechanics are so incredibly abstract in the first place. A "hit point" is not exactly something that always means the exact same thing. Having exactly the same abstract handwave of mechanics doesn't imply the same in-character effects: it's why totally different weapons might roll the same dice for damage despite one piercing and one bludgeoning, or paralysis might be the result of a venom, a magical curse, or a psychic effect.
This abstraction's a good thing. It means you can represent a wide variety of in-character effects without having to devise a new mechanic for each one. I like to take advantage of it.
So why not spend the time used for reflavouring into making slightly different storm based spells?
Because you get more spells via reflavoring. For one, you can reflavor a dozen spells in the time it takes you to create a new spell that's all-but-perfectly balanced with the old: it takes me the same amount of time to reskin a caster's entire spell set (particularly in 4e) as it would to create a new spell from scratch — assuming it was balanced, of course. For another, there are only so many negligible mechanical variations you can get out of one spell if you need them. With reskinning, that's not a concern. For yet another, you don't have to keep track of all those negligible differences; sure, if you like them and they're the point of spellcasting, that's not a downside, but if you like casters with a lot of variety, they add up fast. And of course, reskinning allows you to have personalized spells even without shifting schools: green fire rather than red, a shield spell that takes the form of a transparent face, and so on.
For me, it's far and away the most expedient answer, and the end result doesn't detract anything from the actual game play when the time comes around. I gladly admit that for these reasons, not everyone would want to play in my game, but it's okay. There's only so much room around the table anyhow.
I on the other hand think its unfair that someones spells are much better because he reflavours them someone who doesn't.
I've never seen "much better" come into it, though. Saying that your magic missiles look like writhing crimson serpents or that your fireball manifests as a bright flash in your eye just before it detonates elsewhere never really granted any advantage at all. Sure, you can grant a slight advantage if you want, but I've never seen a reskin that would turn a 1st-level spell into a 2nd-level spell. Those are easy to catch. And villains don't need to be precisely balanced. If you're throwing a 6th-level party against an 8th-level villain for a dramatic fight, it isn't really relevant if his "4th-level" Bloody Sacrifice spell could achieve "5th-level" utility in a situation other than the present battlefield.
I think in order to exert a
much better advantage for reskinning, you would need both a player who is terribly hungry to find every game advantage possible, and a GM who doesn't see the difference between slight advantage and great advantage (or doesn't care). I don't play in groups like that, but I concede that others do. I think that combination will have problems with a lot of things, though, and reskinning is but one of many worries.
We play very combat-and-tactics focused, but refluffing is not a problem, it is a good method for the DM to get interesting monsters that fit into the story. 
