First of all, there aren't any more pop-ups on the new FAAB than there were on the old FAAB. Both have two pop-ups. But let's analyze them both and see if there's a solution here.
The first pop-up on the new FAAB is actually there to speed up the process, not slow things down. But let's see if it's working as planned. Here's how it works: When you select a player to drop, it asks you if you want to copy that drop to all conditionals. This only happens once when you choose the dropped player for the first time. If we don't ask this, then you'll need to tell the system who you want to drop for each conditional bid, which will take much more time than just telling the system that you want to cut the same player. Eliminating this pop-up would default to you cutting the same player in each conditional bid. Would that be better?
The second pop-up happens when you choose to delete a bid. This is set up in the event that someone accidentally clicks delete for a long string of bids.
The old page actually doesn't have a confirmation for deletes, but the old page has a pop-up to alert a user to choose a player to drop, which we removed on the new page.
We also don't have a pop-up if a person submits a bid without cutting a player. When that happens, the bid isn't run because the owner would have too many players. It actually says in your Bid History that you have too many players when that happens. Some owners have already failed to get players they wanted because they didn't cut someone. A pop up there could have saved them!!

We're looking for feedback here to speed up the process for you. Again, if the first pop-up isn't needed, then we'll default to copying a dropped player to all conditionals since you would no longer have an option. You will just have to go and edit every drop if you don't want the same dropped player for each conditional. Would that be better than the current setup?
The second pop-up seems pretty standard on all sites: Confirming a deleted bid. That's a safeguard that seems to be needed to avoid costly mistakes, isn't it?
We are open for discussion and suggestions here and it's your FAAB system, so let us know what you think. We can make changes here where needed if they are needed, but at least you understand why the two pop-ups are there. Thanks for any feedback here.