As a DM who has to take high-level gaming into account, I don't allow "self-stacking" the metamagic feats unless the caster actually took the feat more than once. For instance, the Twin Spell feat is almost completely useless if you allow someone to "double-empower" a spell with only the Empower Spell feat.
Furthermore, think of the Wizard 21 (or Wizard 7/ Incantrix 10 if you like) who has access to Improved Metamagic. He casts an Empowered x4 Cone of Cold. That's 45d6 damage. Compare this to Meteor Swarm, a "normal" 9th level spell. See the imbalance? My thought on it is that this guy should only be able to do it if he actually took the Empower Spell feat 4 times.
Boccob (and his level 20 spell slot) could tell you that infinite Empower Spell should be a Salient Divine Ability, not a feat. I can see a god pummelling someone with an Empowered x15 Cone of Cold for 112d6 damage, but I don't think even epic characters should do it without Epic Spellcasting!
EDIT - Of course, Boccob would probably just Empowered x12 Horrid Wilting for 150d8 non-elemental damage in most cases.