Hmm... maybe maybe not.
It depends on the class feature really.
Even if thats a design flaw its a design flaw in the minor really.
Take hide in plain sight for instance.
In your suggestion, having invisibility exist would be bad design, and it really isn't.
It just become so when hiding is ALL that a class would be doing.
The deisign of classes that don't do anything except 1 thing or even don't do that thing
well thats the design flaw, imho.
Casting divine power is fine, theres NOT a problem with it, conceptually, its a good thing for the "Cleric of the War God" to do. It only makes fighters feel small in the pants if it automatically makes them better than the fighter.
If feats scaled, and classes ALL classes got level appropriate abilities that wouldn't happen really. Even if you gained the good BAB you wouldn't have the expertise the fighter has because of his plethora of feats that benefit from the good bab all the time.