I would like to start this off by saying that I really love the rakghoul stuff so far, but I want more. I know that they already kind of closed the story, but more would be great! My favorite idea that I came up so far:
Based off of a heroic on Taris, our heroes go into a lab set up to study the rakghouls' behavior (probably on Taris, but maybe not) to rescue (if republic players) or kidnap (if imperial players) scientists that were overrun by rakghouls in an accident. You face a boss to get to a safe room. After rescuing a few, you have a decision: The first is LS and you choose to take the scientists back to the republic fleet/imperial interrogation lab; the second is DS and you choose to kill them all. If you choose the LS decision, then one turns into a half-rakghoul half-human monster and is the next boss. If you choose DS, then you leave and fight a different boss (I usually go LS, so I didn’t spend as much time on the DS decision.) The other scientists leave to find safety. Anyways, you set out to find out what happened to the lab (through holorecords or something). You discover that a group of activists are trying to “save the rakghouls” and sabotaged the lab. After that their leader enters and you fight him (or her, and maybe some backup, too). You defeat them, and another LS/DS decision comes: Spare them on the condition that they shut down their operations, or kill him to get a step closer to shutting them down yourself. Either way, the FP finishes and you report back to your fleet.
I would love more suggestions, and I'll leave you with a rakghoul emoticon