I have an aftermarket system (Pioneer Avic n1) and if anything the sound is enhanced due to the built-in EQ functions of the Pioneer. Before you do it, make sure the sound shop has the appropriate wiring harness to adapt the after market radio with the shaker system. When mine was changed I had to live with a popping noise for a few weeks while the shop ordered the correct harnesses. All-in-all I'm happy I did it though especially with all of the problems of the stock head unit.
Performance White 2005 Mustang GT Premium Dark Charcoal Int. no IUP
Options: auto trans, shaker 1000, premium wheels, wheel locking kit
Mods:Pioneer Avic-N1 head unit, UPR antenna delete, UPR polished door lock pins, 20% window tint, IUP auto shift ****, IUP Steering Wheel, IUP door sill plates (scuff plates), locking gas cap and counting...