It doesn't need to naturally point. You need to use your sights and dryfire until it feels natural.
For the most part I agree that how a gun feels shouldn't be the only thing being considered...but that doesn't mean you should pick something that feels bad. You could train to shoot just about anything but a gun that points naturally can't be a bad thing, can it?
Maybe the "feel" or "pointability" or "cool factor" makes practicing more enjoyable - that should count for something.