I think metamagic balance is completely thrown out the window if the spell level is not increased.
Course, I think that Arcane Thesis (even the 1 level total interpretation) is not balanced, so to me, the Metamagic Rods are way broken with the spontaneous interpretation, broken with the at prep time interpretation, and ok if they just gave the feat to the caster 3 times per day (i.e. still increased the spell level). In this third case though, the cost would have to come down.
It would be real nice if WotC created some strict balance rules and then stopped side stepping them. The entire feat and magic item structure should be strictly designed and enforced.
They should not have too many standalone feats and the ones they do should be "tier 1" feats. Powerful feats should be at the end of feat trees ("tier 3" or higher) and magic items which hand out feats should never be stronger than the feats themselves. It defeats the entire feat concept of the game to hand out feats with magic items, hence, feat magic items should always be weaker than the feat itself.
Note: by feats here I mean class-like ability feats such as Evasion or Metamagic or Crafting or whatever, not bonus add feats like Weapon Focus which can easily be handled by a magic weapon.
Since metamagic rods are stronger than the feats themselves (with either interpretation), they are by definition broken in my book.