Why doesn't the consistent winner matter?
Because winning Regionals or Worlds has more to do with how good of a player you are then what faction you're flying. It's not like Paul won 3 world championships simply because he flies rebels. Part of that is he defeats Rebel, Imperial and S&V lists. So as long as the top 16 or so shows good diversity in factions then everything is fine. If there was truly a faction imbalance you'd see the top 16 be skewed accordingly.
Survey says (top 10 X-wing lists):
5 Rebels
3 Scum
2 Empire
I'd say that is diverse and history of top 10 lists shows the Scum and Empire have both had their days in the sun.