About good vs evil - that's what the "canonical" story is about, and there will be Good and Evil (and Neutral) in the game, as a way of using the BNW ideology system. But it doesn't have to be the dominant element in the game, as different civs can have different motivations, and there can be conflicts based on different reasons than good vs evil. For example there can be a conflict between Elves and Dwarves based on a "nature vs technology" concept. Of course the actual wars in the game aren't predetermined, but this kind of tension between the races can be a part of the background story.
Actually I haven't thought much about such things, so feel free to make up your own stories
Generally the ethics will be represented in the game as BNW ideologies, so the "tenets" associated with each of them will dictate which things are viewed as good, neutral and evil (some ideologies will be probably blocked for some races, so you can't have evil Archons or good Orcs, for example). This brings up another problem - the player actions can be viewed as good and evil too (for example declaring war on someone without a good reason can be considered evil), and these actions might be inconsistent with the ideology that player chooses. But I think it's a problem for the later stages of development, so we don't have to worry about it now.
Generally I'm not going to pick a similar route to Pazyryk's mod, where the player basically creates a custom civ as the game progresses. I prefer more "conservative" approach, so it will be quite similar to the base game, although the differences between civs will be somewhat bigger. So, like in base Civ5, the UUs, UBs, UIs and UAs will be based on civs, while policies, beliefs and ideologies will be customizable by the player (and the AI will probably use those that fit the racial themes best, using the flavor system). But there should be more UUs, UBs etc. per civ than in the base game.
There is a strategic resource called Magical Power indeed, it will be used for mages, summoned units and city enchantments (which will work like buildings purchased with faith in G&K). This resource will come both from the terrain (Magical Nodes), and some buildings (like Wizard's Towers). About the details of the explanation how magic works - it's up to you
I think I talked about this with rocklikeafool, IIRC we determined that there should be a minimum of 5 unique units+buildings per civ. Generally, I don't think all the units should be unique, but there should be much more of them per civ than in the base game.