The simplest way is to simply shuffle up the tiles, then pull about 60-150 of them for use.
This will typically mean a 1-3 hour game, depending upon player speed and exact number of tiles.
It also limits the needed table space.
It does, however, also mean it is possible to not have any tiles turn up from a given expansion.
Also, don't use the River nor River II, nor the Count.
The River I & 2 simply lengthen setup and increase think-time needed at start....
in addition to taking time to start, and adding 10+ tiles each.
The count, by allowing reinforcement as it does, really adds to tactical think-times.
If using princess and dragon, you may want to hold out one volcano, and shuffle it into the play stack after generating the ones you're going to play with.
This way, you know the dragon WILL show up, but might not be showing up twice.
Same for Tower tiles from The Tower.
boardgames.stackexchange.com/users/1047/aramis
I probably wouldn't use the River in a 2-player game: it acts to rapidly expand the available playing area and gives the players more "elbow room".
This may not be really what you want with just players, as it just means you may end up doing your separate things at opposite ends of the table.
I'm a big advocate of Traders & Builders and Inns & Cathedrals as adding a lot of strategic depth of the game, and I definitely wouldn't recommend removing them from the mix.
You could try trying to add a time limit to your play - obviously you're now playing with over 100 tiles total, so if you're regularly taking over a minute to choose your move then of course you'll be looking at a 2-hour game.
Or else you could agree to stop after half an hour or an hour or whatever: as long as all players got an equal number of turns then there's no real harm in calling time, right?
boardgames.stackexchange.com/users/436/thesunneversets
If it is just two of you use a chess clock to force yourselves to play faster.
Play with the rule that if anyone runs out of time then they cannot play any more tiles.
We play with a multiplayer game timer that I wrote for my mobile phone, and we (3/4/5 of us) can get through 3 games with the basic set in an hour.
Before we had the game timer, we could drag out a game to well over an hour, and to be honest it was pretty tedious.
boardgames.stackexchange.com/users/1927/Andrew Gleadall
You could just not use all of the expansions at once.
Instead, pick one or two expansions, maybe at random, every game.
Now there is variability, and each game will be different, but you don't have a ton of extra tiles and rules in play in any given game.
This is how collectible card games like Magic the Gathering, or deck building games like Dominion, manage to stay enjoyable, despite having tons of expansion and variability.
You don't increase the size of the game, or use all expansions at once, but rather each game you play can be played with a different set of elements but still within approximately the same level of time and complexity.
boardgames.stackexchange.com/users/112/Brian Campbell
The best way to increase variability without impacting game length is to focus on the aspects of the expansions that do not involve tile drawing.
For example, you could use the base set (with or without the River), the large followers from I&C, and the builder and pig pieces from T&B, which would add most of the options without changing the length of the game.
boardgames.stackexchange.com/users/2259/VolcanoLotus
An excellent 2-player method for lots of expansions: Use a 30-minute timer that is out of view of both players.
Use all expansions you own mixed together in a big bag (The Traders and Builders bag will work).
When the timer goes off, no more tiles or meeples can be placed.
My wife and I are no strangers to Carcassonne expansions.
We regularly play with: The Phantom, Inns and Cathedrals, Traders and Builders, The Princess and the Dragon (without the fairy), The Flying Machine, The Messages (without the second scoring meeple), The Ferries, The Witch and the Mage, The Gold Mines, and the Cult.
We use colored dice on the scoreboard instead of a meeple, because we usually “pass go” 4-5 times each in a 30-minute game.
We roll a die to see who goes first, then the first player chooses how to start - selecting one of the following: the original starting tile, the River, the River II, or the City of Carcassonne.
We start the timer when the setup is ready and then play our hearts out until the timer goes off.
Cleanup is easy.
Just take out the starting tile(s) then shuffle the rest back into the bag.
We've tried lots of different methods over the years for balancing expansions and play-time, and this is definitely the best we’ve found.
Because it’s only 30 minutes, it stays fun, and we often have time to squeeze in a second board game.
boardgames.stackexchange.com/users/18744/Ned Strong
My wife and I were playing Carcassonne last night with several of the expansions and we found that the game was taking a ridiculously long time.  We had the base game, the River, Inns & Cathedrals, and Traders & Builders all in play at once.  I am hoping to find a way to minimize the tiles in play without sacrificing the variations created by the expansions.  Any suggestions?
How can we use multiple Carcassonne expansions without the game taking forever?
boardgames.stackexchange.com
<carcassonne><expansions>
boardgames.stackexchange.com/questions/5093
boardgames.stackexchange.com/users/798/Vinnie
Shuffle the tiles and pull out a limited number to use. Don't use the River in a 2-player game. Use a timer that is out of view. The best way to vary the game without impacting length is to focus on the aspects of the expansions that do not involve tile drawing, or just pick one or two expansions, maybe at random, every game. Alternately you could agree to stop after half an hour or an hour or you could use a timer. The simplest way is to simply shuffle up the tiles, then pull about 60-150 of them for use. Also do not use the River in a 2 person game.
The simplest way is to simply shuffle up the tiles, then pull about 60-150 of them for use. Best not to use the River in a 2-player game. You could agree to stop after half an hour or an hour or you could use a timer. Another option is to pick one or two expansions, maybe at random, every game. The best way to increase variability without impacting game length is to focus on the aspects of the expansions that do not involve tile drawing.