I think the main reason we won't tier Mega Evolutions separately from their unevolved counterparts is the fact that our tiering system centers around usage statistics. In order to be tiered correctly, we have to go off the usage of the base Pokemon being used in battle.
In this regard, tiering all of the Megas separately from the base forme creates a situation in which we are tiering ~28 Pokemon based solely on "power level" rather than actual usage. EDIT: There's a distinct disconnect, I'm not sure which would be more affected, the base or the Mega, I think the base.
Bans are the exception, and as fusx points out, we only ban what is broken in its simplest form. Hence, we ban the Mega Stone if that is in itself causing a Pokemon to be broken.
The reason we want to ban the Mega Stone rather than the Pokemon as a whole is that we are banning only what is broken (the Mega Stone) and not a combination ban (Mega Stone + Pokemon), or worse, a subset in-battle Pokemon (Mega Evolution). I won't delve into the particulars of the Blaziken ban, because that is where the simplicity aspect of the broken clause comes into play and not for the scope of this thread.