Because it was a canonical pairing with a really great back-story (not to mention a canonical tragic break-up), more than you usually got in the cartoon. It pairs up the second-most-dangerous Decepticon with the second-most-dangerous Autobot. What's not to love here?
I can't make S1-2 Starscream work with S1-2 Skyfire, though. He's too unrepentantly mean, too much the treacherous, evil Decepticon, and very unlikely to forgive Skyfire for "betraying" him by deserting the Decepticons, not to mention embarrassing him in front of Megatron. And S2 Skyfire very obviously got over any inhibitions he had against blowing Decepticon Seekers into widdle-bitty bits.
However... S3 Starscream is a 'whole 'nother kettle of fish'. We only see him for two episodes, but he's definitely mellowed out compared to the old Starscream. Less vicious, a bit more fun-loving--though his ideas of "fun" are major headaches to everyone else. He actually tries to help out an old friend. (Save me from his idea of "help", but he tried). He seems indifferent to Autobot vs. Decepticon, now--all he cares about is Starscream vs. Galvatron.
I also see the hypothetical S3 Skyfire as very lonely and emotionally vulnerable--most of his old friends are 9 million years gone, the Cybertron he knew is 9 million years dead, and thanks to the events of TF:TM, most of his new friends and his one surviving old friend/lover (Starscream), are dead.
Thus the possibility of reviving an old friendship into a new friendship/romance.
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I can't make S1-2 Starscream work with S1-2 Skyfire, though. He's too unrepentantly mean, too much the treacherous, evil Decepticon, and very unlikely to forgive Skyfire for "betraying" him by deserting the Decepticons, not to mention embarrassing him in front of Megatron. And S2 Skyfire very obviously got over any inhibitions he had against blowing Decepticon Seekers into widdle-bitty bits.
However... S3 Starscream is a 'whole 'nother kettle of fish'. We only see him for two episodes, but he's definitely mellowed out compared to the old Starscream. Less vicious, a bit more fun-loving--though his ideas of "fun" are major headaches to everyone else. He actually tries to help out an old friend. (Save me from his idea of "help", but he tried). He seems indifferent to Autobot vs. Decepticon, now--all he cares about is Starscream vs. Galvatron.
I also see the hypothetical S3 Skyfire as very lonely and emotionally vulnerable--most of his old friends are 9 million years gone, the Cybertron he knew is 9 million years dead, and thanks to the events of TF:TM, most of his new friends and his one surviving old friend/lover (Starscream), are dead.
Thus the possibility of reviving an old friendship into a new friendship/romance.