No ready-to-play adventures. There are some adventures, but most require tailoring, especially given the large differences between PCs and especially for advanced PCs. If you want to run a D&D game, you can purchase a "campaign in a box" or string together a few bought adventures and you're basically done. If you want to run an Ars Magica game, you pretty much have to invent it by yourself. Which leads to....
Difficult to design adventures to. If you want to design a D&D adventure, you just look over the Monster Manual, build up a strong of encounters, and embellish with stories. The CR-rating and encounter design rules pretty much write the adventure for you, with the monster manual serving as inspiration and creativity pump for putting the plot together. If you want to design an Ars Magica adventure, you're pretty much on your own. There is no system in place to help you put one together, and to pump your creativity as you're doing it.
Lots of book-keeping off-screen. Ars Magica is built for players that like to tinker with their characters off-screen, advancing them and making magical items and so on. Lots of players don't want that - they want to play the character in-game, not to mess with baroque mechanics out-of-game.
Lack of tactical game. You don't get to play the tactical mini-game like you do in D&D. Combat is more abstract and often more monotonic, and tends to involve the environment far less as magi are just too powerful to care about it and as there are no rules or tropes for incorporating it. Add to that character vulnerability (often in an immune/dead dichotomy), and you get very brief and intense combats but ultimately ones far less rewarding and dramatic than the more slowly escalating HP-chiseling and the movement/ position / environment dependent combat in other games.
Badly written rules. Fifth Edition is great, but even that edition suffers from serious vague language and unclear rules; the rules are simply not written with an eye for technical writing. In many places the editing falters too, placing important rules in weird places, unemphasized in the middle of the text (quick - what's the key mechanical advantage of many powers invested in a familiar bond, which isn't mentioned in the familiar section?). The magic system is very flexible but not at all defined enough in many ways, so that in practice there are no guidelines for a lot of what players will want to do and that will create lots of arguments. This one really hurt my last game, as the players grew very frustrated with vauge and undefined rules.
Unbalanced game. Ars Magica characters are so diverse and non-standardarized that often one will be very effective and everyone else not. This breeds boredom and frustration as everyone wants to be effective. And yes, of course perfect balance cannot be achieved - yet still, in practice a D&D group will have a balanced party where everyone meaningfully functions in combat and has its own clearly-defined role to play in it and in the roleplaying leading up to it, and the game will be about combat; whereas an Ars Magica party will more often have one or two characters that really dish it out in combat, with the others just trying to survive or, at best, give them cover, and the game will often not be about combat (which, for some players, is a minus) and PCs will be so diverse and personalized that they won't have very defined roles in or out of combat.