Yeah, this is a really fun feature, but it's not well suited to an RTS game. Designing a vehicle can take quite a while, so unless you can design while the game is paused, it's just not very feasible.
If you want to check out a game that allows this, look for Pax Imperia: Eminent Domain. It's loads of fun to play. Huge tech tree with lots of areas of specialization. You can of course research everything, but it takes many hours, so usually you'll want to concentrate on a certain area to get your edge over your opponents. The game is very customizable, and it is real time (largely), but the amount of customizations required means you might very well end up trying to play it in a turn based fashion. (You're allowed to enter commands while the game is paused).
The only part that sort of annoys me, is when a battle occurs, everything outside of the battle is paused until the battle is complete. The battle proceeds in real time though. You're essentially playing on two different time scales between general game play and battles though, which seems to be why they pause the rest of the game like that. It takes a lot less time to move about the vicinity of a planet in combat than it takes to fly all the way across the solar system(s). This becomes annoying late game if two powers with 100+ planets are at war.
One way I can think of to get this idea to work in a real time game, is to let players create custom vehicle setups before the game starts (as well as during), and to provide them with a default set so they won't need to do this setup to get playing the first time. As you research the techs used in each vehicle, you unlock that vehicle and get to build it. Also, since this vehicle design process can be time consuming, you'd want to save the setups across games so they don't have to be constantly redone.
