When we play big games we always use 2 or 3 base games (depending on how big). We have played games with two of all the expansions, with the exception of only one of the Count, the Plague and the Catapult (which we don’t like), and its works fine I think.
I agree that the Wheel of Fortune, the Catapult and the Bazaars disrupt the game. But as we like to play a little aggressive we always include the Count and the Plague. They maybe have complicated rules, but when you are used to play with them I don't think they interrupt the game so much. In regards to the King & Robber, I think it's a matter of how you keep track of the longest road and the biggest city. We use designated meeples as King and Robber on the scoreboard for this.
In my opinion, the most interrupting game component in a big game is the Barn. In a big game you don't want your meeples stuck on the fields for the entire game, but you don't want to loose your big farm either (Dragon, Tower, Plague), so of course you use the Barn when a nice field emerges. But this gives the opportunity for all the players to get easy points with small connecting farms throughout the rest of the game. We have had games where the farm with the Barn has been scored 6 additional times with connected fields. This really interrupts the game
In the end it boils down to what type of game you like to play. But I think it's a good idea to always use 2 or 3 sets of the base game if you play with multiple copies of the big expansions.