Actually, the later 2:1:2 systems are producing numbers equal to the top 2:1 systems. So the choice really moves away from performance to what one prefers in looks and sound.
Personally, I prefer the looks and sound of duals and am converting the RH TDs on my 107" '02 FLHT to the later under carriage exhaust system with a Fuelmoto X-pipe and their 4" Jackpot mufflers. I have to admit that I love the sound of the RHs and hope the new sound is as appealing but I will also admit that moving the heat from the rear exhaust head pipe running right under the seat is very appealing for a south Texas rider.
True duals would be the last choice for me even though I am currently running a set of RH TDs on one of my bikes. The later merge collector/x-pipe 2:1:2 systems had not been proven when I went the TD route. If you prefer the looks and sound of a 2:1 system, both RH and/or V&H have good offerings. However, if you want to retain the look and sound of duals, a set of V&H slipons like the Monster Ovals would wake things up, or you could take the next step and match those slipons up with the V&H Power Dual head pipe for better results.