Right, well, they did make a sequel, though.
Honestly, I've never played them, I was just in the first grade when the second game was released, and I moved on to my SNES by then, too. However, reading about how the game was built, it looked to use the formula of Super Paper Mario, what with the chapters and all, but with the gameplay of The Legend of Zelda.
From what I recall, Nintendo Power always made a big deal about it, and the game did well enough to merit a sequel then. Unfortunately for the sequel, the NES was about dead in '94. Remember, this is two years before the 64 and the same year Donkey Kong Country was released. Had the game been a year or two earlier, it may have made a larger impact and the franchise wouldn't have been killed.
Essentially, I think a Kid Icarus game is coming. There is too much interest in Pit. Far too much interest than any other old franchise. However, past that, I think StarTropics would be the game that could make a very simple and intuitive transition into today's games, from what I've read. It's praise then, unfortunate release timing, gameplay and story ideas, as well as obscurity really would allow developers a great structure to follow, while granting amazing liberties, too.