I have never seen concentration used for non-spellcasting purposes. So I have no problem with merging Concentration into Spellcraft. Honestly, I'm a big fan of merging skills.
However, I understand the complaint about Int replacing Con for the application. Int isn't as important as Con is for the other spellcasting classes. In that vein I agree that the attribute bonus be based on the spellcasting ability.
Come to think about it a lot of the combo skills include skills that were previously powered by a different ability.
As for the idea of combining either Knowledge Arcana or Knowledge Religion with Spellcraft, that actually is a much more complicated game mechanic. What if a character multiclasses? What happens then? What about new players? There are new players who get flummoxed by just the 3.5 player's handbook.