Not sure if it's a spoiler since it's a theory, but based on what's been happening...so if you aren't caught up in the show and don't want spoilers...stop reading.

I think that things are going to start changing for Eddie. His relationship with Iris is falling apart because of Barry in part. I foresee him finding another girl and having a kid...and then maybe dying because of Barry in later seasons. Maybe he had to choose to save Eddie or Iris or someone else. This is the anger and hurt that Wells/Thawne is feeding on and what caused him to get stuck in the past (yeah it was Barry, but it was because of his hatred and vengeance).

I think we will see Iris start to try and pull info out of Barry/Eddie on who they are working with (Flash) and in doing so Eddie will feel threatened and betrayed, destroying their relationship. Barry will try to convince her to stay with him and she will think kindly of Barry and those feelings from the time travel episode will resurface. Over episodes to come, she will hang out with him more and get close to him maybe start dating him. This will fuel a fire for Eddie's hatred of Barry and will be the point where Wells is trying to remove Barry so Eddie has a better life.

Now that Barry knows though...i'm not sure how but they will work on forcing Wells to appear as himself...Thawne. Physically that is. Some kind of tech that will remove Wells' DNA from his body. This starts the event of Flash chasing RF and hunting him or catching him for a short time.

Also, I can easily see Tina replaced Wells in the seasons to come...along with Barry's father getting out of Prison..maybe a spark between them...haha.

Or I could be COMPLETELY WRONG. We will see.