Frankly, I've got similar problems with metamagic. First, that it has this weird binary feel to it. If metamagic were free and strictly better, you'd use it for everything. As it is, it's neither free nor strictly better, so you avoid using it at all for the most part. When you don't actually pay for it (either via class features or magic items), metamagic can make things very interesting. Many of my casters, for example, carry around an empowered spellshard attuned to ray of enfeeblement. That's an encounter-bender right there (not strictly a breaker, but definitely a bender).
I think it stems mainly from the relatively broken magic system that 3.5 has in general. Despite the feel of it, there's no application of universal design principles. A well-designed magic system would do two things: first, it would better-quantify effects and correlate them to power levels. You should be able to "annoy" foes at this level, "disable" them at another level. Broken magic comes into 3.5 when you can get access to stuff early due to poorly-designed spells (I bet the designers thought of glitterdust as anti-hiding/invis magic, not an encounter-ending will-save or suck AoE at SECOND LEVEL), or when you can accelerate the power curve. Blasting might be an officially inefficient use of spells, but an arcane thesis'ed searing blistering flaming explosive empowered fireball can do quite a lot of "battlefield control" in a 20' radius (lots of corpses = difficult terrain).
Honestly, there's just not enough variables in play here, all we have are save DCs and spell slots. If it were more like psionics (power points and psionic focus), you could do a bit more. But imagine a system where a metamagicked fireball had a lower save DC. Or one where there was something else - you needed to make a spellcraft check or whatever, similar to truenaming but not stupid. The core system doesn't play well with metamagic because there's not enough ways to pay the price for using it.
What I've been seeing in practice is that people avoid metamagic in general, but definitely use it on the one or two spells they have as their "signature" move. The fire sorcerer has AT:Fireball, the dread necromancer has AT:vampiric touch, and so on. To be honest, this probably ends up working out okay. I wish wizard casting was a more elegant system, but I don't think we need to give them MORE power in the current environment.