All I can say is that the original cutscenes made me wet my pants at the time. I would have threatened my parents to go on hunger strike unless they bought me a Sega Mega Drive/Genesis--if I thought it might have worked. I know I wasn't the only one. When the edition with 3D cutscenes came out... Well I don't even remember or probably didn't even heard about it, I know it didn't have nearly a fraction of the impact.
Which version one personally likes better is of course a matter of taste and it's absurd to say that someone is wrong. Anyway I for example bought the remake of Sid Meier's Pirates!, and I do think that it's a vast improvement across the board, except for one thing: the 3D women are so much uglier than the ones in the Gold edition (even the "beautiful" ones)...
At least the ships are prettier, but I really prefer women...