I know that the CivConverter can convert scenarios and graphics from MGE format to ToT format, but I'm not sure if it works the other way round. It also doesn't have a GUI, so it's completely command-line based, and I can't make it work correctly with the XP command line interface. But I know it works in DOS, since I've already used it to export my personal modpack from MGE to ToT. The screenies I posted earlier are from that modpack.
But there's no way I'm backing off from using ToT now. Compared to MGE it has a lot of functions that improve scenario making a lot, like the new way of handling unique units and techs. ToT has native support for that stuff. It doesn't include a graphical editor though, so you have to edit the text files directly. But that's a challenge I welcome. I'm a bit experienced with it already.
Another reason not to use MGE is that we want two maps, a surface map and an underground map. That just isn't possible to do with MGE.