Huh.. since nobody answered it... Red Alert and Dune 2000 had actual voxel 3d models, and raytraced models for buildings. Warcraft 2 had paint over raytraced models.

I suggest you to start with 3d model first, because isometry is hard to do by eyesight, and for RTS you will need a lot of sprites and directions. Moreover, there are perspective and non-perspective iso. I.e. in Warcraft 2 some sprites had perspective, while pure isometry is an orthogonal projection. There are also various kinds of what people call "isometry" (it is a buzzword now): many RTS games use military projection, which is also used by Ultima Online, while Diablo used modification of proper isometry:

https://en.wikipedia.org/wiki/Isometric_computer_graphics#Differences_with_%22true%22_isometric_projection

Given that your first task would be setting up the type of projection you will use, but that is of course after you figured out your setting, story and art direction.