Hmm. A though choice. I consider both of them very hard, and they are more harder if you challenge them with Terra, since his evade ability is pretty bad. So lets analyze these bosses.
Mysterious Figure, an time traveling troll is really hard. Almost everyone of his moves kills you with one hit without second chance and once more. He has all kinds of attacks raging from a long combos to casting meteors and mega flares. Furthermore he can rewind back time, and gain back some HP during the process. You basically just spam dodge roll the whole fight.
No Heart his also really difficult, but unlike Mysterious Figure, his regular attacks won`t one shot you. Although this dosen`t really matter since most of his attacks are deadly combos with MX`s Keyblade. Combining this with his updated speed, he becomes even more dangerous. Sometimes No Heart is so fast, that I can`t react to his moves at all. He also has this attack which is similar to one of Sephiroth`s moves. He flies up to the air and casts an massive explosion. It leaves you to low HP, and puts all your commands to reload mode.
So both of these super bosses are hard, but I think for me Mysterious Figure is harder. You have to have good endurance since dodge roll spamming will numb your thumbs. Also he can take your commands away with tornado, and a single mistake can ruin your good run. Thank God in the Final Mix version you can escape his whip attack.