Yes, a true 3D system is nice but that is tough on computers of course. all the calculations involved. I was just expanding on the 2D world by larian in DD. But yes, it could certainly work. In that case true octagons can be used. I sippose my idea could just as well use 'stop signs'. A 6 sided area or hexagon. It makes no difference.
It is interesting to be able to the areas come alive with some kind of magic that you can see. But won't everything start to glow of magic? I kind of like just the plain tree and herb etc. I would use you ideas as a skill you gain to perceive magic that is in all things. Something to switch on and off just to check what sort of magical properties the land around you has. So you can find a good piece of alnd to battle on, lure if the AI allows them there and have enough mana for the kill.
I do like it that dark magic can ovecome the natural magic in the land. But that could be the whole quest for a whole game rather than that evil roams about and destroyes the land. I don't see a point in it unless you come accross a dark wizard that despoils what he wants and that you have to fight him/her in a quest. Othewise I see no purpose in having areas that grow 'dark' all the time.
As for heaven and hell.. I don't know. It sounds so...already done. If you have a DD game with already sea and air added to the surface and the underground already you have plenty to explore. I prefer for myself other realms, like the one where the Imp is with the Bees and Wasps.
