This is a good hypothetical question... I guess I'd make a distinction between how good I judge an album to be (e.g. if I was doing some sort of ranking list thing) and how good it is to get a certain album. Compare an album of just 5 songs, all amazing, to one with 20 songs, 10 of them amazing (on par or better than the 5) and the other 10 really bad. Obviously the second option is better because instead of 5 amazing songs you have 10, but if the second album is half bad I would still count that against it if I had to say which is better. How much they count it against it varies though - change them to 10 songs of average quality and I might still say the second album's better overall, even though the average quality is technically lower.
But as a whole, unrealistic examples aside, I absolutely do think having great songs makes up for having some not so great songs, that an album being too long isn't really a valid criticism for me (unless taken to ridiculous levels where it becomes incredibly difficult to get to know every song), and that an album flowing well or being good to listen to all the way through is a bonus that doesn't automatically make it better than an album of excellent songs, and that counts for very little if there are no great songs on the album.