Just like RIRFIB/RIBFIR I see the Jetfire/Skyfire debate as pointless. It's very clear who Jetfire and Skyfire are within context of the medium discussed.
Just as I call Rumble 'the blue guy' when I am directly referring to the cartoon, I refer to the name Skyfire when I am referring to the cartoon character.
If I am discussing the comics or toys - I refer to the character's name as Jetfire just as Rumble is the red guy as far as the toys and comics go.
That's how the characters were officially named in those respective mediums.
Of course an individual fan has every right to call the character whatever he/she likes but that is just personal preference.
When it comes to Jetfire and Skyfire being distinct, of course they are - One is the character in the cartoon and the other is the character in the comics/toys.