2:1 or 2:2 with a crossover benefit because of scavenging exhaust and cutting down on reversion in the midrange. Straight drag pipes (2:2) are what will give you the most power at wide open throttle, but most people don't run at wide open throttle all the time, and you lose midrange power due to reversion. Baffled 2:2 pipes give you good low end torque (cuts reversion in lower rpm), but limits your wide open throttle. Adding a crossover between 2:2 exhausts helps assist scavenging in the high rpm and improves top end somewhat (but not as good as open drags). 2:1 pipes that are baffled give you good low end torque, keeps the midrange because they reduce reversion issues, and scavenges exhaust better than 2:2 baffled pipes, so wide open throttle improves and you get a wider performance gain. All that being said, if you're running baffled pipes, whether 2:2 or 2:1, you're not going to see significant differences except on the top end (wide open throttle). This is in general of course, because there are so many different pipes (length, diameter, type and size of baffle also affect power). So, pick the pipes you want for your bike 2:2, 2:1, whatever and tune accordingly.

 

Why do you think you have to change exhaust? On my 03 Heritage I installed HD bagger hardbags. Used stock headers with SE11 mufflers.
Later changed to V&H big shots, then V&H pro pipe. All worked fine with HD bags.

 

from my actual experience...with the build I've listed in my sig, minus the 2-1 cats, but with samson true duals I had 76HP 88TQ. Switching to the 2 into1's gave me the numbers in sig.
I was in same mind set as you. I dropped all tis $$ on a build and I wanted to get the MOST out of it. Thus the 2n1 pipes.

 

That's my fault. Should've been more specific. My goal is stretched. Standard bags would work just fine. I'm shooting for baddad fender ans stretched bags. Not saying it's never been done but I've never seen stretched with same side exhaust except shorties that cut off in front of the bags. I have seen 2:1 with a cutout on that side only but not over under like mine. I'll be getting Samson, hopefully they'll get their sh*t together in the months ahead so I can do it this winter.