I'm going to post POSSIBLE SPOILERS FOR FUTURE EPISODES (and I include huge spoilers from a scene that was shown in a couple of promos for the next episodes, along spoilers for a couple of other shows, I've covered all those spoilers with "blackout" tags, but I'm warning you all just in case). Most of it is just me theorizing about what I believe that will be the future of Eddie, but if I'm right, these could be the biggest spoilers regarding this character.
Ready?
Eobard is going to kill Eddie and will replace him using the shapeshifting device.
If you have seen the promos for this season's last episodes you must have seen the scene where [BLACKOUT]Eddie kills 2 cops in cold blood. Some people thought that he could be under Grodd's mind control, or that he could have been working with Wells all along, but now I'm sure that Eobard is going to kill him and replace him.[/BLACKOUT]
When Eddie was casted for the show, I thought he was going to be the Reverse Flash, the actor had recently played villains in other CW's shows like "The Vampire Diaries", and with that last name, Thawne, I was sure that he would be The Flash's nemesis. Then I watched the pilot and I thought that Eddie could still be the RF and Wells would be someone else. I thought Eddie was pretending to be a nice guy and dated Iris just to piss Barry off, knowing she would be his future wife.
Then I read the script for "The Flash" movie that was written by the same people who run this show, and I could see all the similarities and how the RF pretended to be a mentor figure for Barry exactly like Wells, and how Iris was engaged to a nice guy that was unrelated to the RF. Then I was convinced that Wells was the RF, but I was still wondering why Eddie was a Thawne instead of some random guy like in the movie script. The actor playing Eddie commented that we would be surprised in future episodes, and Grant Gustin said that there was a plot twist that nobody has seen coming just yet.
Then it was revealed in the last episode that Eobard is using a shapeshifter device from the future to take the identities of other people like Harrison Wells. It always bugged me how Cavanagh looked nothing like the guy playing Eddie, but the actor playing the "real" Eobard does look exactly like a "distant relative" of Eddie, and it fits the RF's mythology from the comics where he changed his face with plastic surgery, I had previously thought that maybe Eobard had plastic surgery to look like Wells, but the shapeshifting device from the future is a better idea, and it also explains why the blood samples in Barry's house didn't match Wells'.
In shows like "Fringe" and "Alias" (both from JJ Abrams) could be seen similar plots where certain villains could completely change their bodies to become clones of other people, in "Alias" there was a genetical therapy that could change all the cells of a person to become a clone of someone else, and that was used by a villain to [BLACKOUT]kill one of the protagonist's friends and replace her, and no one could notice it since she was an exact genetical copy of the girl she had murdered and replaced[/BLACKOUT], and in "Fringe" there were a group of villains that were shapeshifters from a parallel universe/timeline that could change their aspect to become clones of other people by using a device that was pretty similar to the device used by Eobard in "The Flash", and one of those shapeshifters [BLACKOUT]killed one of the protagonist's friends and replaced him[/BLACKOUT], the writers just repeated the same plotline that they previosuly used in "Alias".
When I saw Eobard's shapeshifting device, I immediately remembered the shapeshifting device from "Fringe" and how in those two Abrams' shows the villains [BLACKOUT]killed a friend of the protagonist to replace them[/BLACKOUT]. Then I also remembered the scene from the promo where [BLACKOUT]Eddie kills the 2 cops[/BLACKOUT] and came to the conclusion that once Barry tells Wells that he knows that he is the RF (there are pics from next episodes where [BLACKOUT]Barry, Oliver and Firestorm are facing an unmasked RF[/BLACKOUT]), Eobard will probably be defeated and will escape somehow, and he will use the shapeshifting device to "hide in plain sight" again (nobody else knows that he has that shpaeshifting device from the future).
And since he knows that Iris is the woman that Barry loves, I'm sure that he will kill Eddie and will replace him, becoming this way his own "distant relative", which makes sense since all the cells in his body change to become exactly like Eddie's, so once he has descendants (not with Iris, obviously), they will be Eddie's descendants from a genetical point of view, there is no paradox that makes impossible that he is his own "distant relative" since we know that the shapeshifter device copies all the cells from other people to turn Eobard into a clone of whoever he wants to replace (like in the other shows I mentioned), that's why when he changed to become Wells, the blood samples in Barry's house didn't match with Wells' blood even if they both are Eobard, now he has Wells' blood that is not the same blood that could be found in Barry's house because that is blood from his original body, and once Eoabard becomes Eddie he will be a genetically perfect clone of Eddie, so Eddie will still be his "distant relative".
The shapeshifting device will probably be destroyed somehow and Eobard will always look like Eddie from that moment on and will keep that identity, he will eventually have children using Eddie's body (not with Iris, I repeat, but with someone else, don't know who), and this will explain why the Thawnes will hate the Allens in the future. Some people thought that it would be because Iris would leave Eddie to be with Barry, but Eddie has proven to be such a nice guy that it would be impossible that he hated Iris or Barry just for loving each other, he could be angry and could punch Barry like he did, but he couldn't become a villain, much less start to [BLACKOUT]kill cops in cold blood[/BLACKOUT] and become Barry's enemy.
Eobard will kill him and replace him, and once Iris learns what happened, she will obviously be sorry for the real Eddie that died, but will have the chance to be with Barry without looking like a b*** for leaving poor good Eddie.