Seeing as how this thread is asking for opinions I'll offer mine. I always tell folks who don't want to do anything more than a basic Stage I upgrade to stick with their stock head pipes and buy a set of slip-ons. Lots of different ones out there. If you're doing a stage II upgrade then a set of true duals is the best bet although again using the stock head pipes and a set of slip ons works fine if you're not looking to get the most out of what you do. Lastly, if you're into a full blown I wanna be the big dog on my street Stage III build, then the best bet is a 2 into 1 system. A handful of companies have recognized that bagger folks like the dual exhaust look and offer dummy left side pipes.
Here's a few things I've heard along the way that may or may not be true. If you want to debate these go ahead, but I did not claim these to be true, I'm only passing on things I've heard.
Screamin Eagle stage combinations work better if you use Screamin Eagle slip-ons. Thunderheader slip-ons with stock head pipes are actually better on baggers with torque builds than some true duals. The best head pipes to use are Bassani, so even if you want to use another brand of muffler, go with the Bassani head pipes. Basanni makes the best 2 into 1 system for a really Hi-Po motor. (Dave Mackie recommends Bassani) I personally debate the last one where V-Rods are concerned. IMO the ONLY 2 into 1 for a V-Rod is a Thunderheader.
Big B