Not much really. In the sense of a mufflers primary purpose is to muffle the sound, a resonators purpose is to change the tone by cancelling certain frequencies. If removed they both will increase the sound of the exhaust and change tone. Some vehicles react better to one or the other or even both.
Turbo vehicles react well to deletes as the turbo itself acts as a muffler, as well as a restriction.
My Balt SS sounded amazing with a muffler delete. My FoST it was ok, should have deleted the resonator or at least changed it. The FoST had a huge resonator and deleting it with a muffler delete sounded ok but was a little much. Exhaust is preference really and sometimes it takes some tuning or in the case of my Balt SS you luck out big time with a $50 mod that comes out awesome. Even catbacks are preference as well, my friend has 6K in his 350z just in exhaust alone between 4 systems trying to achieve the sound he wanted. So far from youtube videos I'm not very impressed with FiST muffler deletes, again though Youtube isn't your best bet as reference (as my 350z friend lol) Going to a meet is the best way to get exhaust ideas.
Plusses to muffler deletes, Cheap, Easy, less weight.
minuses, None really on a Turbo vehicle just have an open mind and you can usually achieve the sound you want from messing around with aftermarket resonators, or mufflers and still end up with a less expensive system then a CBE.