if you are meaning dumping it and leaving the factory muffler on then yes it will sound crappy. Don't get me wrong it will be louder than it is now but not what you are looking for.
Try this one day when you get boared. take off the muffler off at the forward clamp and just let it hang. get in and start the truck and listen...you may like it enough not to spend any money on it......i did!!

 

Just incase you are wondering i say that it will sound crappy because i tried it. i started at the farthest clamp and worked my way up taking everything off until i liked tha sound. and thus all i hae is the factory dual cats and y-pipe. granted i am cheap!!! despite what i get paid.

 

I want to dump it now, but I will wait to see if my dad likes the idea.
As for the muffler I probably just get something that is free flowing and the muffler shop has in stock.
If I do get a pretty free-flowing muffler does the brand of it affect the performance, and sound?
If my exhaust system ends up running this free will that hurt my overall performance?

 

Good idea! I would not have thought of that. I'll try it when it warms up here in Ohio.

 

You could do what I did. I took the front resonator and the muffler off. Im running a straight pipe from the y-pipe to the rear resonator. Sounds mean as hell, cost me SIGNIFICANTLY less to do, and still got some decent power gains.