So with the alignment system and choices you make. Will any of that impact you way later down the line.
Like say you decided to kill that final boss you run into instead of say arrest him. So later down the line will you run into a character that is hunting you down or causing you trouble only to turn out that this character was say the brother of that boss you killed and they want revenge.
Or maybe you show mercy and let that boss go. So later down the line you are in a big boss battle and that boss you showed mercy shows up and aids you in the battle as a way of repaying you.
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Owner and Big Sister of the Justice Girls -Champions Online-City of Titans-
Forum Breaker
Leader of the Ellysyn Dark Ensemble
Skyrim used something similar - they called it their Radiant Questing System. I'm not involved with tech so I don't know if a system like that is being pursued, but it has been done before, in other games.
There is a huge team of Lore and Story writers. I'm sure the idea of choices coming back to haunt you will come up. We still have two years at least before things are fully developed.
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Personal rules of good roleplay
1.) Nothing goes as planned.
2.) If it goes as planned it's not good RP