I would say that they are fundamentally the same system, and that the same is true with PF. True, there isn't 100% compatibility. Maybe only 80%. But as someone who has played most of his AD&D adventures converted to 3.5 I would say the conversions really aren't that much. I mean, Construct BaB changes? If the DM remembers the rule it takes 5 seconds to change. If the DM fails to remember the rule, who is even going to notice?
More to the point, the systems are close enough that there is a high degree of player compatibility. Most people who play PF would play and enjoy 3.5, and vice versa. If no one can publish 3.5, and no one cares enough to promote games of 3.5, at least we can carry on with something 3.5 like.