S&S carbs are easier to tune, and modify. Mikuni's are a little tougher to dial in, and there's NO reason to modify them, as they offer 3 different bore sizes. 1 thing with a Mikuni that gets missed by the first timers, is the choke pin. You need to use the 1 that comes with the carb not a stock CV Harley choke pin. Also you'll need a bracket to hold the choke cable, An air cleaner adaptor, for bolt on air cleaners, and you will also need a manifold. The Mikuni manifolds are power losers( the short turn at the carb entrance is HORRIBLE). Power wise, size for size, they're about equal, with a good intake manifold for the Mik.
John