I'm pretty sure we can all agree that Metamagic feats, as they are, suck. The all carry several hefty costs to any caster that takes them (spending several feats, increased spell levels) and another hefty cost for certain casters (increased casting time for Sorcerers and Bards). They carry several costs, with relatively low benefits (few people will choose an Empower Magic Missile over a Fireball or Lightning Bolt, or a Maximized Fireball over a Disintegrate or Circle of Death). However, to do away with any of their costs would make them far TOO powerful.
Frankly, I think the increased casting time for Sorcerers and Bards is a load of crap. None of my games have such a rule.
The increased spell levels seem to be a necessity to keep balance... to lower them, let alone get rid of them entirely, would unbalance the game and make spellcasters all uniform in their uses (if you even lowered the costs by 1, every single spell would thus be Silenced and/or Stilled, and almost every spell would end up being Empowered due to the low +1 level cost). Any sort of daily limit, although possibly limiting the power, wouldn't really make sense in-game and could end up being even more tiresome and annoying than the costs as it is (for example, I went through City of the Spider Queen last year with some friends, most of which were spellcasters... at many points, they were infiltrating the bad guys' city, and there were times when every other spell they'd cast would be Silenced and Stilled for fear of being discovered- in a case like that, they would much rather have given up a spell level or two rather than have a daily limit). So taking away increased spell levels would cause more problems than it would solve.
Then, of course, there's the feat cost. Now that I think about it... what if there were no feat cost? Or, at least, a more limited number? Such as you simply took one "Metamagic Ability" feat, and from that point on, you could use any Metamagic feat at will, as long as you could spare the spell levels? It may seem powerful... but if enough people are complaining about the spell level cost, can you really see more people using Metamagic spells than already do, just because there's only the cost of one feat? Also, if Metamagic feats were more accessable, I can definitely see more fun and more use coming out of them. After all, do we really need to spend four or five feats we're never gonna use? What's wrong with one feat you're never gonna use that encompasses all the others?