Well, I've ran a campaign from 1-20, and the wizards had Energy Substitution in my game and it worked just fine.
Firstly, can I state that none of the three (!) PC wizards took Energy Substitution. Granted, they were a transmuter, necromancer and enchanter, but even so, this still shows that it is not clearly overpowered. You spend a valuable feat in order to get Energy Substitution: it is therefore implicit that it is slightly better than its ordinary counterpart, but not so much better as to bump up the level. If it were no better, then who would take the feat? To say that no additional benefit should be derived is similar to calling Improved Initiative broken because it makes your initiative better than if you didn't have it (or Weapon Focus etc.)
As for Sonic energy, this is no big deal. Silence and/or countersong will negate it, and if you have a wizard who starts going berserk on Sonic magics, as soon as the enemies get wind of this they are going to have a lot of Protection from Elements [Sonic]. Granted, monsters are less likely to have Sonic resistance than Fire, but intelligent foes can prepare accordingly- and for the majority of foes with no resistances or only resistances to certain elements it makes little difference. The only time I can see it clearly overpowered is with the Elemental Savant prestige class: though this is more the fault of the Savant than the feat itself (and note that you cannot get [Sonic] savants...)
To summarise, it is a powerful feat. But feats are both handy and limited and some more power is meant to be derived from it. Even the dreaded [Sonic] is easy to defend against with bards, Silence or appropriate Energy Resistance spells. It's good, but not too good.