Ok, first off I think it should be entirely 2D, like Diablo and older versions of Civ. This cuts down on resource use and system requirements.
Second, I think it should be started with the civ-like component, since I envision the diablo-like components being essentially spawned from that whenever a battle happens. You'll want the basic civ battle decision system in place anyway for those who don't want to diablo it, so this is a sensible starting place. Put in a simple resource collection and domination game (there are already a number of Flash-based examples, although none come readily to mind in URL form just now), and then you can build hack-and-slash battles and ultimately perhaps multiplayer on top of that.
I think you begin with just a few resource types, a very limited technology tree (if any - probably make it static, not research-based), and a smaller world map. Have limited unit types (maybe 5 typs of units), limited weapons, etc. Basically start everything small and limited, but try to get as many in there as possible.
Get it all setup and then work on balancing once it's functional.
Use publicly available textures and art at least as placeholders while prototyping. Keep it in prototyping phase, including prototype art, until you really want it to be played a lot (i.e. when it's a bit more mature).
Those are my thoughts for now. Unfortunately I don't have any Flash dev experience. Another possibility would be Java btw.