But to be fair, the 3.5 DMG warns against the very kind of metagame thinking you're describing here (see "Metagame Thinking", p.11). We are also told, "The ability to use the mechanics as you wish is paramount to the way roleplaying games work" (p.14). Granted, that section goes on to urge DMs (especially inexperienced ones) to be careful about tampering too much with the rules--which is reasonable advice for *any* RPG, I would suspect.
Except it doesn't. It describes metagaming as thinking of the game as a game and making decisions BECAUSE it's a game.
There is a difference between "I made a spellcraft check and I know that in this world the only spell that can give you a permanent enhancement is Wish. If you drink multiple rounds in a row, it should give you more bonuses because that's the way the Wish spell works. Also, I know about creating magic items and an item like this would cost HUGE amounts of money." and "The DM is forced to use Wish for a magic item like this, since there's nothing else in the game that does this and he's using the magic item creation rules, so it'll be expensive."
One is perfect role playing and the other is metagaming. Even if they end up exactly the same. The example given in the DMG is the perfect example of this. It explains about a player saying "We should search for a way to disable this trap, because the DM wouldn't put a trap here without a way to get around it." which is metagaming. But it explains that if the player said "Let's search for a way to disable the trap because the people who built this place wouldn't have put in a trap without a way for them to get past it." that it wouldn't be metagaming.
So the idea of a magic well that automatically enhances a player's ability score(s) is perfectly acceptable within 3.5, both according to the letter and the spirit of the rules.
It says that it's good to use the mechanics how you wish. It never says you should use mechanics you make up as you wish. The mechanics say what spells do, how to make them into magic items and so on. In fact, if I was to paraphrase the section that says you can change the rules, it says "You can change the rules, but they work absolutely fine the way they are, and it is better to find interesting ways to use the rules as they exist than changing the rules or coming up with new ones. Plus, since the rules all work together to accomplish the goal of the game, a change of one can have disastrous effects on the rest of the rules. So even though you think it's a good idea, it's still not a good idea. But if you are absolutely, completely, 100% certain it's a good idea then go ahead and change things."
Which is a far cry from "Sure, go ahead and make up a well that gives you a permanent bonus to the strength score of anyone who drinks from it."
The philosophy of 1e and 2e was closer to "There's no RULES about what kind of items or spells exist. If you want something, do it." which caused a lot of things I didn't particularly like, balance wise...but it did create a more open game.
4e gets back to that feel in some ways without opening up EVERYTHING. It says(essentially), "If you need something to make an interesting plot, go ahead and do it...don't let the rules stop you. But a ritual to make the world explode might exist...it just shouldn't fall into the hands of the PCs. Don't treat the rules as the 'physics' of the game world...don't assume that just because none of the classes in the book can do something that it can't be done. Don't assume that if a ritual doesn't exist in a book that it can't be made. But use it only for NPCs and let the rules keep the PCs balanced."