Now that we know exactly what's going on with Wells it seems to me as though not only did Thawne absorb the physical characteristics of Wells, but he must have absorbed his memories as well. Maybe this is what has made him more sympathetic towards all his "friends". It may even be that the real Wells' persona exists somewhere inside Thawne and is exerting a certain amount of influence over him without his knowledge.
If the rest of the team finally figures out the extent of what's going on with Wells maybe Barry will find a way to save the real Wells in the past and bring him to the present. Then Cisco and Caitlin could find a way to reverse the process Thawne used on Wells and transfer all of the memories Thawne accumulated acting as Wells back into the real Wells. That would allow the show to keep Wells as a main character while still keeping Reverse Flash around for future use.
Or something. I'm probably getting way too elaborate with this theory.
Given that Firestorm is a two-in-one deal, why the eff not? And maybe Firestorm technobabble can help extract Wells.