User blog comment:IamJakuhoRaikoben/Sorcerer Magazine, Issue 30: June 2014/@comment-4489126-20140702021537/@comment-7716957-20140702043146

Since Mega hasn't justified the answer ( -___-)~ And I kinda thought of the same answer, on skype. >_> but mega answered here first...

The answer is Jude.
 * "You didn't cry, for years gone by" -- for the years since Lucy left home/disappeared; rather she was happier in FT Guild. She didn't cry or long for her father (well until she realised he died.)
 * "The relationship I missed" -- Jude was too obsessed with his business to realise he was not being a proper father to his daughter.
 * "If only I hadn't been so cruel" -- Jude was such a jerk father to Lucy after Layla died, scolding her for that rice ball T^T and demanding money when he was broke etc.
 * "Your pain would not exist" -- well her pain from having to leave home (cause she said it hurt to leave the place where her mummy was laid, the servants who loved her etc), and then her pain/conflicting feelings when Jude died.

I hope this is correct :D