Perlin noise is cool, but why not try to fully simulate plate tectonics, weather patterns, drainage? It would go a long way if deserts were in the rainshadow of mountain ranges, islands corresponded to real volcanic activity, etc.
I guess there is a limit to what you can do with the chunk-by-chunk approach, but I think a certain type of minecraft player stays basically put within a couple dozen chunks. Having worlds "load" on exploration would be a worthwhile tradeoff.
I get that this is a hard, but it is interesting, and it's a problem that would captivate an intelligent developer. They have like a million dollars, why not?