This was very clearly made in a time of economical despair for Disney. This movie comprises two separate animated segments - "Bongo" and "Mickey and the Beanstalk", both originally intended to be full-fledged features but cut short due to restraints on money, resources and time.
The music in both segments is increasingly average and forgettable. The "Bongo" segment is lightly enjoyable, but poorly animated compared to Disney's usual standards. To top it all off, it's pacing is mind-bogglingly dreadful (it drags on forever).
Before we get to the next segment, there is an eerily strange live-action bit in which a ventriloquist who was popular in the 1940s ties the stories together with the help of a little girl and two of his (creepy) dolls. The movie proceeds into "Mickey and the Beanstalk", which is not all together terrible, but certainly not the brightest moment of Mickey, Donald and Goofy. Neither of these three is really used to their full potential, save for some slapstick here and there. Annoyingly enough, the ventriloquist, his dolls and the little girl keep commenting on the animated segment off screen. To say this really destroys whatever fun there may have been in the segment is putting it mildly. The "commentary" is incredibly annoying.
In the end, though in a historical perspective "Fun and Fancy Free" could gain our respect, I feel that its one of Walt Disney's lesser efforts, and certainly the weakest animated Disney movie of the 1940s. Go see it if you want to say you've "seen them all" - otherwise, there's little "fun" to be found, and you'll mostly get the feeling you're watching something that was thrown together and launched into cinemas as a desperate attempt to get some money during the tough wartime.