I was thinking about this, and at first I was very excited.
I see the advantage of this: If the rushing QB is in the game you can run different AI, or if the other team puts in a specific HB for pass plays, all that is great. The DC in me was excited.
Then the OC in me started to think how to exploit this. It seems like it'll be pretty easy to exploit. Put in your rushing QB to run a FB dive, etc. Teams will have to be more creative, but I think you can set things up in a way that it is too difficult to make these settings worth much.
Then I began thinking again as a DC. The new inputs for this is going to be ridiculously complicated. I think it's much more than the "if their rushing QB is in the game, run this play where we blitz our safeties." You will have to create a bunch of different inputs and place them all in a pecking order. Think of all the combinations, based on personnel. If your opponent has their rushing qb, their receiving HB, and their blocking FB all in the game, only 1 input will fire, unless you create all of the possible combinations.
In lower levels, a throwing QB has enough strength to actually hold is own at TE. You're simply going to see teams putting in the rushing QB for a lot of other HB or FB run plays, as well as some screens and passes. You'll see the speed HB in the game for FB dives, etc.
So, in essence, a smart OC will be able to get around the tagging system, which means the DC has to be pretty much prepared for everything regardless of tags (unless an upper level QB really can't throw at all), which means the whole tagging system won't really add anything to the game at all.
The more I think about this, the more I realize it's something that will appease all of the people calling for it, but won't really offer a viable solution against well coached teams.