So what would you do??

I think they will be ok at 3. good luck tonight talking with your fh let us know how it goes.

How old will they be? Maybe have them be 'honorary' flower girls? They can dress up, and depending on how they feel they don't 'have' to walk down the aisle, or maybe they can walk down with your aunt before the whole bridal party comes out, like when they parents walk down? Ask your aunt to play it by ear that day. Worse comes to worse, you just have picutres with them. As for the reception, maybe your aunt can either bring someone (I know an extra expense but it may be worth it) that take the girls if they aren't having a good time or make a scene or something? When my cousin got married, her sister's baby was a few months old. So the sister's in laws came to the wedding, and once the baby started getting tired, they scooped him up and left.
HTH and good luck. I'm a daddy's girl too and it kills me not to do stuff he asks.