Haven't we talked Pizza before several times?
Tim's Pizza is a mom and pop place on US 40 in Southeast corner of Independence. Good pie, I think they may be a cash only business.
Fun House is also on US 40 Highway in Independence. Hasn't changed in 40 years. Great pie, especially the canadian bacon. It's the real stuff.
Minsky's franchises are independently operated. The one I go to on MO 291 in Independence is good. I really love their chef's salad to go with a pizza. Great stuff, but pricey. Some of the other Minsky's around town are not as good.
Independence Square has a funky little pizza place called "Square Pizza." It's pricey, but also makes a good pie.
I've been to Brucsco's out here in Overland Park. It's OK. Had a calzone for lunch. Old Shawnee Pizza is OK too, and you can find coupons on their website. Rosati's in OP is OK too.
http://rosatisop.com/
All of the above are better than your chains like Papa Johns (evil Donk loving bastards), Pizza Hut and Domino's.