The primary complaint people have with old forts (and, indeed, new ones) is related to low frames per second. Simply put, when the game runs too slowly, it really isn't fun anymore. Some people find that 40d runs significantly faster than the newer versions, even discounting the change in the size of any given map, so they find their forts remain fun longer on 40d than in 31.x. Given that creatures were increased in complexity as well (so, presumably, each individual dwarf causes more FPS drop due to tracking body parts) it isn't really surprising.
There's also the matter of increased complexity. Many people find the military and alerts system in 31.x to be hopelessly complicated, and either cannot or will not learn how to use it. Military was vastly simpler in 40d (and far more powerful, as mentioned). Health care was made more complicated as well, which is an additional worry for many people.
Also, in 40d, the megabeasts were both less common and less powerful. It's uncommon, but not unheard of, for a single Forgotten Beast to wipe out an entire fort with a deadly syndrome, but in 40d they didn't actually exist, and dragons, hydras, bronze colossi, and... I want to say there was another form of megabeast, but I'm blanking on it... Anyway, megabeasts were about equal to a reasonably-competent, decently-equipped dwarf in a one-on-one fight. Now, a reasonably-competent, decently-equipped dwarf is likely to die against a megabeast (they're more powerful in combat), but even a legendary hero with fantastic equipment might do a mutual kill against a Forgotten Beast with deadly dust or other deadly syndromes.