There is a fine line between an intense challenge and a retarded waste of time... My suggestion for the ultimate super boss would be:
1. Don't make him a requirement to beat the game.
2. Don't make the fight take more than 30 minutes.
3. Have different evolutions which require different tactics, follow different attack patterns, and have different weaknesses than previous "forms".
4. Have the boss pause attacking in between evolutions to call in some quick sweep and clear mobs to keep the player motivated, excited and feeling like a badass. Make them progressively harder... part of the boss battle themselves.
5. Don't give the boss instant game enders unless the player screws something up.
6. The boss should have several ways it can be defeated... let the player assess the situation and take it out using his/her own tactics. Don't make it a trial and error type of ordeal... I shouldn't have to die 15 times just to learn his secret patterns in order to beat him... common sense should be one's best ally in order to defeat it.
7. Make a hard boss without making him immune to certain attacks... let me use my menu.
8. If there are blow-away moves, I should have a chance in between evolutions to get a party member back if I play my cards right.
9. The best challenges are those won by perserverence... give me a real battle through the trenches, not a handgun against a nuclear missile launcher.
10. Since the battle will be long, give me several turns per 10 or so minutes to heal up and buff up my party, and unclench my butt muscles.
11. Make it accidentally epic.