I don't think Hydaelyn is a villain, nor do I think Zodiark is villainous in the classical sense. I think they are both superweapons that have been turned against each other by opposing sides that are only fighting because their methods of saving the world differ. I also believe them to both have been co-opted by a third unknown force that perpetuates the conflict. As was pointed out in the story, Zodiark's heart was born of Hope. Hydaelyn's was born out of duty. Venat only wished for Zodiark's strength to be kept in check. Both of these reasons do not seem evil to me.
"Light, Dark, doesn't matter. What matters is how you use it."
In monochrome melodies
Our tears are painted in red
(Bleeding to the edge)
Deep inside we're nothing more
Than scions and sinners
In the rain
Do light and darkness fade
Hydaelyn is slowly becoming too weak to stop Zodiark from breaking free of his shackles. But I wonder if he even has the strength to persist if His heart is no more. What of Hydaelyn's heart? I'm inclined to believe that Minfilia/Ryne are the remnants of the one who chose to be the vessel for Her in the days of the Ancients. "For those we have lost. For those we can yet save." Is a mighty fine mantra to remind yourself that self sacrifice is necessary if it means saving others. Minfilia herself was swept away to be used as a vessel to keep Her strength from growing weaker. This implies that she has an extremely close connection to Hydaelyn. Hydaelyn refers to Minfilia as a "beloved daughter" (Ryne being fragment of the same soul of her current vessel) and allows their merger, with Ryne becoming the new Oracle of Light. Looking to those who have walked before to lead those who walk after.
The 8th fight in Eden has an extremely important message in it's lyrics. That merger was no coincidence when you consider the color of her hair changes depending on which form she was currently in. Shiva retains her silver hue. While Hydaelyn/Venat... Was a blonde.
Turn the light on
And let her in. Won't you
Turn the light on
Turn the light on
You'll never win 'less you
Turn the light on
Turn the light on
The pain won't end 'till you
Turn the light on
The soul longs for oblivion, oblivion
Falling too far for the fear to embrace me
A voice from the past screaming there is no end (no)
A slave to my fate, ever doomed to repeat this
again and again and again and again (yeah, I'm)
Falling too fast, no it won't overtake me
A voice from the past echoes loud like a drum (oh, yes)
no more goodbyes, though my heart is still aching
Now open my eyes, one more time, Here I come