I really have no idea, why you do not let casters use higher level slots for lower level spells... these spells are typically a lot weaker, how can this be abusive? This house rule is especially harsh for sorcerers, who only know very few spells. You should double the spells known for spontaneous casters then to make them worthwhile to play under those rules...
Anyways, you could easily make your system work this way...
Add a limitation, that you cannot cast a spell of a level - including the metamagic spell level modifier - higher than the highest level you can actually cast. So, a 11th level wizard could cast a quickened 2nd level spell, but not a quickened 3rd level spell or higher.
Also, change the cost to a spell slot of a level equal to the metamagic modifier, for example, "Quicken Spell" requires a 4th level slot.
A wizard (prepared caster) would have to prepare the metamagic feats like spells and can use them on any prepared spell, as long as the above limit isn't broken. Then wizards can use the feats a bit better (more flexible application), but still have to prepare them. I'd also require a move action to prepare the metamagic feat in addition to the standard action (or whatever it is) to cast the spell (this replaces the casting time increase for spontaneous casters, but applies to all), after spending that action, the next spell you cast will be metamagicked appropriately (if it doesn't break the above limitation), but you must "use" it during the current (or following) turn, otherwise it is wasted. A sorcerer (spontaneous caster) already benefits from it in a different way, as Crothian pointed out above. So both have their share then.
This way, there is also no abuse with breaking the spell level cap (which can get ugly pretty fast), and the cost is pretty reasonable, too.
One thing you have to think about is magic items and meta-metamagic feats and abilities (like Divine Metamagic, Instant Metamagic).
Also Heighten Spell and Fortify Spell could be a little problem for wizards, maybe it would be ok to allow then to use only part of the prepared metamagic feat (but use up the full slot, of course)... this means... like prepare a 4th level Heighten Spell (+4 spell levels), but if you want to heighten a 4th level spell to 6th level (the highest you can cast), then you can still use it, it's just that the other +2 are wasted.
I'm tinkering with a different approach, based on the UA variant, giving each metamagic feat charges per day (number depends on how powerful the feat is).
Bye
Thanee