Plane Sailing said:
Sir Whiskers: The issue for me is not rules crunch for doing an x/day limitation, but rather a descriptive reason for such a limitation. Cleave doesn't have a limit per day, nor do most feats. Stunning fist does, but that seems a silliness in the feat - there is no reason given why it could only be used a limited number of times per day. (yes, I know, it is for "balance" purposes. To my mind an x/day limitation is a blunt instrument for balancing an ability and suggests that someone couldn't think of anything better. I want something better

)
Unfortunately, if you don't like limiting these feats by x/day, you may be back to requiring them to increase spell levels. The feats, as written, are really too good to allow them to be used all the time, any time, just for the cost of a single feat per metamagic ability. IMO, there has to be some sort of limitation.
Some ideas off the top of my head:
You could add an XP or gold cost, but then wizards would be even more loathe to use these feats than they are now.
One possibility is to allow the feats to be used freely, but increase the casting time of any spell using them one step: standard action becomes full round, full round becomes one minute, etc. Of course, I'm not sure what to do with Quicken Spell under this plan, and that's the one I'm most concerned about for balance reasons.
How about this: each time a caster takes a metamagic feat, he can select one spell to apply it to. In effect, he's learned a new spell. Each time the caster levels, he can select another spell for each metamagic feat he knows. The spell(s) selected must be cast-able by the caster, e.g., he can't apply Quicken Spell to
magic missile until he's able to cast 5th-level spells. I know this isn't the same as your original idea, but it might be balanced enough to use in play.
One last possibility: create a specific feat chain for metamagic feats, which must be taken in order. Once selected, the feat can be applied (with no level increase) to any spell known by the caster (of the correct level, of course). This way you could limit the best metamagic feats to higher-level casters, minimizing their impact.
As for rationales, I can think of quite a few for any of these possibilities, so I don't think it would be difficult to explain these limits in terms of the campaign setting. (For instance, a feat chain could be explained the same way as different spell levels: some effects are more difficult to master than others).