I personally like having the Sword of Aeons because it kills most enemies with one hit, But I didn't really like the fact everyone in albion hates you. You could go to the Avo Shrine type deal and pay a lot of gold to get them to not hate you but that would be a waste because Game_Guru's way is good and gives you EXP and items to sell. Also what does your sister do for you if you keep her alive? Do you ever see her again? I've beat it several times and haven't found her after the fight with Jack of Blades.
I Also like keeping her alive. I found a sword that is kinda close to the Sword of Aeons power at Bowerstone(Spelling! Sorry!)North in the shop. Its heavy and has a few agumentations and does similiar damage but cost a pretty penny.
I think its fun to play either way because they both have different things happen!
~TicTac