The biggest problem I think is that they are not proportional in power to the power-creep experienced by using supplemental materials. In other words, in games where only the core rules are used, metamagic seems to get used and has its place, particularly in scrolls and magic items. But compared to other feats and spells from supplements, it can't hold a candle. Thanee said it best - why empower a fireball, when you can use firebrand? Simple answer - if there IS no firebrand to use, then Empowered fireballs are both effective and well-costed.
For a practical answer, in games where supplements are a given, I'd say beefing up is required, possibly just doing away with "Sudden" metamagic and using them as the standard metamagics. Though I must say I like Gez's answer best so far. It shows a consistency that the current system lacks (And quicken spell is most likely overpriced in truth).