This always happens so what I usually remove is anything in the resorts section that doesn't concern the resort we are staying at(unless we plan on resort hopping), anything from Dining that doesn't pertain to PS's I've made or places I think are even on the maybe list, also I go through the planning and front sections that talk about getting to WDW. Anything I've already dealt with I remove. Generally I throw all these extra pages in a plastic freezer bag and put them in the front pocket of my suitcase just in case. I usually can't close my PP either so sometimes I'll use the rubberbands that come from the produce dept on stuff like broccoli.
I don't like to remove the extra yellow pockets b/c I use them for receipts and to keep little momentos like napkins, park maps, anything paper that may get smushed in my regular luggage.