So in this case it is just not good because is realistic that your commander is not supposed to survive destroyed transporter?!

Don't forget to mention that commander can cloak him self, and you can create decoy commanders. All of that makes still grate gameplay, especially in later levels.

As for visuals, it is still incredible on how low machines game was working, and movements of units was great.

Again, you have your taste, and I have mine. In todays eyes game such as colonization looks like dinosaur compared to the new games, but I still play it, same as I play TA and similar games.

I think the game is Wargasm

And what about...
 

...this one: Warzone 2100 (I think the first 3D ground RTS) : http://www.mobygames.com/game/windows/warzone-2100

And if not, it could be WarGames, an older film-themed game from the same year (I think) as Warzone 2100 : http://www.mobygames.com/game/windows/wargames (unfortunately no screenshots on Mobygames, but here: http://www.ag.ru/games/wargames are some - but the page is in Russian).

Tell me if I'm right!