The Quickening is good.

As a stand alone film.

Forget the fact that it destroys the mythology of the first film.

The Quickening works on tis own merit. It has great action sequences, a great villain. The films was brighter, the flashback to Zeist compares cinematically to the flashback to Scotland int he first film. The music and sound effects were good too.

Then we get the Renegade version. *beep* beans what a piece of crap.
Technically storywise it's less bad. Although it kills continuity issues leading into Highlander 3 that i won't get into right now.
But the film itself is completely boring. Gone are the wide angle shots of the flashback, because they needed to hide the Zeist landscape and spacecraft debris. Gone is the quality score, now repalced by Queen songs. The film is much darker and gritty looking so much that it hurts your eyes.
The tighter scene edits are extended or changed so much that its jarring. The bad voiceovers os some the characters. The fact that they changed the planet crap to time travelling dimensions wasnt that much better. And made for some silly ass inexplainable moments in the film.
There were subplots that were added that really didnt need to be there in the first place.

And then there's the special edition version :\
Sure ya cleaned up the effects and redited scenes, but its still not as good as The Quickening.

It's unfortunate that the Renegade version and the Special Edition are all that survive in today's market. Because a lot of the NEGATIVE reviews I see towards Highlander 2, are idiotic moments from the renegade version, things that at least made SOME sense no matter how far fetched in the Quickening.
I don't even have my videotape copy of the Quickening any more. The Quickening version was still being aired on television after the Renegade version hit VHS. But its been years since Ive seen it.

The only other instant of this happening is the Blade Runners directors cut overshadowing the original. But then again this is a good thing.

in the future will these Special Unrated DVD's with extra footage or Director's cut of film's like Alexander and Daredevil that are complete reworks of what was in theatres be the ones to survive?

Check out Daredevil the Director's cut compared to the Theatrical Release.
Much like the Quickening and The Renegade Version. It's two totally different movies. Neither of them being too good on their own. Viewing them together back to back is a great film lesson.
How sound effects and Re-edits and voice overs can change a film Completely.

Sometimes for the better as int he case of Blade Runner and Daredevil: the Director's cut. And soemtimes for the worse as in the Renegade version.