Armada Starsceam and Megatron actually strike me as having anti-chemistry. Megatron comes out and says that Starscream is expendable to him. Starscream is not enough of an issue to Megatron that I would see him bothering with screwing Starscream. That would show that Starscream has enough power over Megatron to make him angry. You don't screw the dirt under your shoes.

Starscream, meanwhile... well, yes, he does crave Megatron's respect, but he snaps out of his idolising in the end and comes to terms with the fact that he fundamentally does not respect that for which Megatron stands. Also, he functions better as a character is he doesn't get the attention from Megatron that he wants.

I think that people see Megatron/Starsceam because they want to see Megatron/Starscream. It's common enough in other series, but I don't feel that it really works here.

What pairings do I see? Megatron/Optimus Prime. They're clear, obvious foils for each other, and Megatron is absolutely delighted to hear that Optimus Prime is alive again.

Sideways/Thrust - what trip down into madness is complete without a little tentacle action?

And the Autobots as a whole are a mess. >_> Hot Shot/Wheeljack! Hot Shot/Sideswipe! Blurr/Sideswipe! Et cetera.