My bike rode great up to 12k feet, only requiring less choke than normal to get it started cold.. and this is with factory sea-level jetting.
Even if it turns out to be an issue, $99 for remote fuel screw adjusters eliminates that problem. And the carbed bike won't have a "snatchy" throttle.. I'd hate to guess what that would cost to REALLY fix. certainly more than $99.
EFI and carbs both have advantages and disadvantages.. Personally carbs, and getting the taller suspension plus almost all the mods I wanted to do (jesse cases, throttle lock, powerlets, SP suspension, decent hand guards, real skid plate, etc) for half the price of a new bike alone was a no-brainer.