Agreed. However, one of the main objectives of hurryup is to prevent the defense from substituting. So rather than have a delay from substituting, there should be restrictions on what formations you can use during a hurryup sequence.
For example, if you are running a 4-wide set, you shouldn't be able to hurryup and change to goal line or a 2-TE set (where obviously you would have WRs at the TE spots). You should be restricted to 4 and 5 wide sets during the sequence.
And likewise, if you are running a set with tight ends, you should be restricted to no more than a 3 WR set.
I'm not saying this is definitely how it should be, but it is an idea to prevent unrealistic hurryup abuse, and in the case of this thread, AI goofs where you have a HB trying to be Peyton Manning at QB.