Some other connections i guess:

Both games had Cave Of Ordeals, but I don't think it was called Cave Of Ordeals in MM.
I think the Twilight Palace and Ikanya Canyon were both very similar. Same kind of music, zombie type characters (after twili people are shrink)
Both Zelda games were said to be the 'darker zelda games'.
Both games that allows Link to transform into something else.