Can you help me understand what it is about a specific piece of equipment having in the past been used for human rights abuse that makes it unsuitable for any future use? It would be one thing if the CIA had operated the flight, but this plane is known to have been transferred to the DOJ long before the flight to extradite Snowden.
Human psychology, the secrecy, the person targeted and the history of lies surrounding the rendition program.
There's nothing inherent about the plane that makes it unsuitable, but people should also be totally unsurprised that it contributes to making people ask extra questions about the flight.
They may have officially transferred the plane, but do you really think that means the CIA would have to stop operating it? I mean it is totally possible that they did, but I could see an equally possible scenario where they just "transfered" it for political cover.
Since the DOJ has been using it for all sorts of non-Snowden business (Google will show you this quickly), I'm not sure where this logic gets you; the same logic suggests any US plane could be a secret CIA plane. That's true, they all could. And?
It sounds like the CIA (and the Obama administration), drawing on past experience, got wise and figured the mission would look less "dirty" if it wasn't a spook plane, but a regular government-registered plane that actually came to pick Snowden up.
But the main point is that adds to the body of circumstantial evidence that some kind of a rendition operation was being planned.
Again: nobody doubts there was a "rendition" planned. Snowden had been indicted for multiple felonies. "Rendition" is what happens when someone is extradited.
It's the preponderance of the multiple factors (as cited in the article), along with the immediacy of the flight and the USG's well-documented predilection for pulling similar shenanigans for the sake of far lesser targets, that are sufficient to raise reasonable suspicion.
And it's the immediate dispatch of the plane which strongly suggests that the U.S. wasn't going to wait to go through normal judicial channels to pick up their target.
I would expect the US to have planned for how to perform such a kidnapping, because dealing with rogue agents in one way or another is very definitely someone's job. I would be amazed if there wasn't a report giving a number of options and pros and cons for each compiled—of course, how it was acted on is anyone's guess.