I’ve always felt this way too.
Of course, I was first introduced to Doom through cartoons, where he was always a general Big Bad (usually fighting Spidey, since most Marvel cartoons back then were Spidey), and then through Secret Wars where he was more than a match even for Galactus and the Beyonder. I love classic FF comics (although I like Ben and Sue more than Reed and Johnny, who I mostly think are unlikeable dicks), but yeah Doom seems way too grand to be limited to “FF villain”, although it does have fun irony to me that Doom is so hung up on competing with a guy who is not even remotely in Doom’s league IMHO.