well supposedly you get better and more even air flow with aftermarket stacks. I have the Graves velocity stacks on my R1 and it helped give me a little more power in my mid range
I also have V-stacks on my 03 R6, but they were made by FactoryPro. the performance improvement depend on the design of the stacks, mine are the 1st generation ones from FP, and they are the short design for all four pieces, which gave me about 4 HP over the OEM ones, but the power gain was in the 11,000-13,600 rpm range so only practical when pushing the bike hard. Graves also offer their version of the V stacks for the 03 R6, but introduced it a year later(2004). Their design is a bit different, they kept the 2 inner v stacks longer, supposely for better mid range power.