Because he isn't the total package, and if you compare his ring work to Flair, Taue, Misawa, Kawada etc he pales by comparison.
A lot of people are primarily familiar with Flairs work in the 90s, when he was past his prime. However, his status as NWA Champion afforded him an opportunity to work all around the world and display his amazing versatility where he was able to work a different style that catered towards that territory.
On the other hand, Bret rarely got that opportunity and had to work the WWF style which was very repetitious. To Bret's credit, he actively tried to change things up which you can see in his matches against Perfect (I'm more of a 93 > 91 type of guy but each to his own), Austin & Diesel. 3 different performances, but unfortunately not enough to compare to a guy like Flair.
On the microphone, it's a no-contest. As much as I like Bret's 97 work, Naitch is an all-time legend and can still cut a killer promo to this day.
The best there is, the best there was, the best there ever will be?
Nope, nadda, not a chance.
Better than Triple H, Shawn Michaels and Kurt Angle?
Yes, easily, all day every day.