El Mahdi
Muad'Dib of the Anauroch
Only problems I see are more work for the DM and whiny players.
The DM has more work to do in order to decide the tone of the game - because modules are certainly going to do that. They're going to determine the speed of play, the difficulty to moderate, the complexity, and the overall "feel". A stripped-down core rules game is going to have a completely different feel than a more anything-goes game. A DM with a job and family is going to have trouble finding the time to do all the necessary prep work to get the dials just right, to stick with the metaphor. If they run published adventures, it's also going to be difficult as the modules themselves will run slightly differently, probably with lots of sidebars making notes, "If you use gridded combat..."
Whiny players, on the other hand...reading around on these boards, I think I'm the only DM with this problem. But the group I play with, what I know will happen is someone will have an idea in their head about what they want to play and if I try to exclude a module for tone or story or pacing reasons, they'll throw a passive-aggressive hissy fit. For example, in my current Pathfinder game I'm running a Greyhawk-set campaign with multiple plot threads that was originally written assuming a good or at least good-ish group and ended up with a bunch of evil and CN characters and had to throw out a ninja, a gunslinger, and a drow. And they whined and bitched and whined and bitched until I finally went with a group that had a monk and a Neutral-to-Evil group. Had to re-write half the friggin' campaign and redo everything from black-and-white morality to black-and-grey. Annoying.
Now say I leave out some of the modules. Next thing I'm going to have is one player whining about me leaving out Module A, another about Module B, and so on until I either put my foot down and they throw a fit or act all sullen, or I give up just to shut them up.
You can take solace that you're not the only DM that has or has had these kind of problems with their group. But I don't think any rules system or module is ever going to be easy or be able to fix this for you because of these factors. The disfunctionality you just described reminds me of my family...and I hardly talk to them anymore!

