Interesting: Large Pro said there was a more "Malicious" version produced by Swizz Beatz & featured the line, "It should've been you in that plane crash" (referring to the plane crash Aaliyah died in)

Apparently the original version of “Ether” made by Nas, was much more agressive and harsher than the one we have all heard. And obviously it has even better lines than the original.

Because Colombia asked him up to 3 times to edit the songs, that is probably the big reason why in certain points of Ether sounds like Nas is filling in spaces with saying things like “cock a fella” and “gay-Z”. I don’t know first hand but this all makes sense because it seems that he was replacing those words with something he had to take out.

And Colombia is probably the reason why people who think “Takeover” is better, constantly bring up the “gay” and “cock” lines that Nas slightly over did it with to make it seem like he lost the battle.

Here's an interview from Fat Joe before Ether was released in 2001 addressing lyrics that were cut from the original song:

AHH: One thing that just came up today, Nas apparently has a response to Jay Z’s “The Takeover” on his upcoming album, which implicates you and Pun and includes the lyrics: “Call yourself gangsta but you were begging for pardon that night in Carbon when Terror Squad flipped on your squadron tried to front on their checks till Pun put a gun to your chest.”

Fat Joe: We gotta hear it but damn, what a way to put me right in the middle of the beef huh? We don’t comment on that, that’s old news. Like I said all the negative energy all that sht you can throw that out the window.
Nas is crazy. No question that we are allies with Nas Escobar. We love Nas. I almost named my son after Nas. As far as him and Jay Z with the beef: that’s they stuff. Until somebody tries to involve me in that sht, that’s it. I ain’t got no problem with the whole Rocafella. It’s well documented. Everybody keeps trying to get me to talk about that sh*t in every interview. Why don’t they ask Jay Z that stuff? I read his interveiws, nobody asks him. If you interview him, ask him.