This is a good graphics update, but however, it should be a per-map setting because many maps were made with the flat 2D graphics in mind. Their tilesets reflect that, with graphics techniques to create the illusion of multiple floors for example.

This also changes the gameplay because the player needs to adapt to the different rendering and how the map appears in their screen. In flat 2D we can always easily pinpoint our shoots through multiple tiles, in 3D that's not really possible because the walls and obstacles appear "tilted", if you get what I mean.

So, here is how you should proceed with this:

1) Make it a per-map setting, so both 2D and 3D maps can co-exist. This avoids breaking and ruining previously created maps.

2) On each 3D tile, make it possible to set their height (seems like you already did this, as shown in the video) and if possible a different texture for their sides. If no separate texture is provided for their sides, then the top texture will be used and thus scaled according to the 3D tile's height.

3) For 3D maps, make it possible to create multiple floors and map them separately, this also makes 3D stairs easy to make. That if it's feasible, because it requires extra coding and you probably don't want to do that. It would be a killer feature though and would completely change the map making landscape.

But well, I think you should focus on more important issues first. This graphics update can come in another game version.