Soundwave in TFP only has Laserbeak although Laserbeak looks more like Ratbat than Laserbeak. I also do not know what happened to Frenzy or Rumble (keep in mind Transformers Prime takes place in the same universe as War for Cybertron)

One thing Fluttershy and Soundwave would have in common would be their love for animals.  

Also, Soundwave took a code of silence.

Soundwave isn’t shy. He doesn’t talk much, or at all in that incarnation, but that’s because he has little to say. He’s easily the most cold-blooded decepticon, both in terms of a lack of emotion and a lack of mercy. He spends most of time at base because as good as he is in a fight, he’s more valuable using his technical skills out of combat.
 
He has exactly one thing in common with Fluttershy, but for opposite reasons. Unlike her, when he wants to deliver a message he does it by beating the tar out of the recipient until they get the point.

Why?

In fact any pony would be a better fit then Flutershy.

@gamerlord  
Then you don’t know ANY version of Soundwave very well.

Fluttershy is a better fit for Soundwave methinks.