The novelization says Tony has modified the plane with Repulsor Ray technology, so, it actually flies faster than the Iron Man armor.
And I don't think we'd see Mark VI actually being built. If you watch the Featture Trailer again, you'll see a scene of Tony adding the triangular reactor and making other modifications on an Iron Man holographic sketch right after he rediscovers the new element. I believe the scene would actually go like this:
Tony rediscovers the new element.
He adds it to an Iron Man armor, alongside some other modifications and tells Jarvis to build it.
While Mark VI is being assembled, Tony builds the Particle Accelerator and energizes the new element.
After he receives the call from Vanko, he asks Jarvis to show him the Mark VI status. It's nearly finished. All its missing is to finish the painting of the arms and legs. Tony sees it and says "Oh, yeah". Decides to paint the rest latter.
But that's just my guess.
And the "I want one" scene with Tony and Pepper was in it.