I'm with you all the way on this one Thanee.
Core metamagic in it's current form does not provide much incentive to select any of the feats with a +2 or higher slot increase. The problem with core MM is that comparative level metamagic'd spells are just less effective than other spells of equal spell level in damage output and utility. Simple as that.
What the core MM doesn't factor is that with an increase in spell level there is an exponential increase in power. A 9th level spell isn't simply 9 times more powerful than a 1st but is many, many times better than a 1st level spell. The same holds true for a 5th level spell vs a 1st level spell, and so a quickened metamagic spell will never be able to compare in power to a normal 5th level spell.
My only suggestion for handling spontaneous metamagic for spontaneous casters is two-fold:
(1) What immediately comes to mind (besides giving the sorcerer a few bonus metamagic feats, something I instituted at 10th and 20th levels for the class

) is to first, leave the metamagic feats at 3/day across the board. The higher the slot increase for MM feats only serves to limit the MM feat to use with lower level spells and makes it balanced across the levels for all the metamagic feats to make it balanced to leave them all at 3/day.
For example, in one day, with a 9th level wizard, we might see 3 quickened 1st level spells and 3 empowered 3rd level spells. I've found the quicken spells for example to be no more powerful than any of the other metamagic'd spells due to the fact that lower-slot-MM feats may modify higher level spells and the higher-slot-feats only get to modify lower level spells. To my surprise the inherent balance we found was almost elegant, since the more powerful MM feats could only effect the less powerful spells and the less powerful MM feats could effect the more powerful spells.
(2) Upon leaving the MM feats at 3/day each, my best suggestion would be to synergize a sorcerer's selection of metamagic feats such that for each MM feat the sorcerer selects they recieve an extra +1 use/day to use for any of the MM feat(s) they possess. So a spontaneous caster who selects:
Silent Spell
Still Spell
Empower Spell
Would have an extra 3 use/day that they may use on any of the three MM feats they possess, in any order.
A SC with but one MM feat:
Energy Substitution 4/day
and an SC with 5 MM feats:
Silent
Still
Empower
Maximize
Quicken
Would have 3/day for each feat plus 5 more uses/day in any order of the MM feats the SC possesses. Thoughts on this one Thanee?
It's flexible and the SC that is more practiced with metamagic benefits from his/her own mastery of it.