There was the Total Annihilation RTS and while it had the normal 2d overhead view, all the data was in 3d.
A Swedish gaming clan put together an accelerated full 3d engine to replay Total Annihilation recorded demos. As it got more and more features it was realized that most of what was needed to play TA was being recreated so they closed the loop and made it into a full game engine which they called SpringRTS. There was the default accurate TA game code but there was also a very popular mod that was not afraid to change things a bit, basically "we like Total Annihilation but also think it could be better" and they called it Balanced Annihilation. We are almost there. BA lived under the Spring project for a few years, but really when you think about it there are ip problems with it using the TA assets, also, I suspect someone wanted to do engine work but was having a hard time with upstreaming it, so it forked off the Spring project, they rebuilt all the units(same unit different skin) are doing a ton of great engine work and called it BAR (retronymed into Beyond All Reason but I suspect it originally stood for Balanced Annihilation Reborn or something like that). So BAR is basically a highly modified legally distinct Total Annihilation.
Zero-K is another great RTS based on this engine. It drifts further off the TA formula than BAR does.
"Currently in development". It's got robots.
"Shut up and take my money, I'm making a donation" :)