the best way to beat yunalesca is 2 use Aeons. protect against zombie and mega death.

anyway, i personally count Seymour Fluz as the hardest story only compulsory boss.

and if u cant count Penance, Dark Aeons or monster Arena, then i vote for Pal version Omega weapon. definitly the hardest boss outside the big three areas i mentioned above, with his 999,999 hp he woud have been a worthy last boss.