This addition to EMPIRE is a clear case for what I call the "Law & Order" mentality. In "Law & Order," they don't waste time or slow down the episode to show the cops driving down the street, getting out of the car, stepping onto the sidewalk, walking up to the front door, and ringing the doorbell. There's no practical need to show that. They just cut right to the point. Just like on "Star Trek," they don't always show someone beaming up from the planet every time. If you've seen it enough times, you can move forward without seeing it happen. Granted, that was likely done to cut down on the effects budget, but regardless of that, it's not needed to show how someone gets from point A to point B everytime. You can put the pieces together yourself.
Vader says, "Bring my shuttle." This means he intends to be leaving, and with everyone else making their escapes from the planet at this point, you'd assume he also is leaving the planet. Then, a few minutes later, he's on the bridge of the Super Star Destroyer. Simply conclusive.
And yes, the entire sequence damages the pacing of the film's climax. Even a fellow filmmaking friend of mine, who prefers the prequels over the OT and likes most of the SE & DVD '04 alterations agrees with me on this point. The film, at this point, is trying to build momentum in a seemingly hopeless situation. Intercutting with the shuttle's journey kills that momentum. Why Lucas chose to add this? I do not know. I do agree that Vader appearing on the Executor bridge maybe could've benefitted from a more proper entrance, and perhaps that was his irritant with the scene. Doesn't bother me, never has, but that's a maybe.
-NJM
