I removed all my logos, nameplates, etc. Then the bike looked too plain to me so I had custom Yamaha lettering made for the lower fairings. The bike looks very clean this way IMO. I can stand those little tuning forks everywhere.
Normally I'd take all the design decals off. I like to leave the YAMAHA on the bottom fairing and maybe an R6 logo if it looks decent. Sometimes taking all the logos off can make the bike look naked instead of clean IMO.