Yea but Aikman didn't win one Super Bowl, he won three, in 4 years at that.
If he won them under some flukey circumstances like Eli did, as a bus driver who floundered around for the rest of his career, that'd be one thing, but a QB winning 3 Super Bowls in 4 years is no fluke and that alone elevates him above only a handful of the most elite players the organization has ever had.
Ware was an excellent player, and he was probably more elite relative to his position than Aikman was, but at the end of the day he was the QB of 3 Super Bowl teams in 4 years and he wasn't Trent Dilfer-ing his way to those titles. There's no way you can put an elite player with an otherwise mostly forgettable career (as a Cowboy) above that on an all-time list of Cowboys.
I also disagree about Romo, perhaps if he had won a Super Bowl, but definitely not if he just made an NFCC appearance. If that were the case you might as well throw Danny White on the list.