Why does Barry Allen's greatest enemy, Reverse-Flash, still have the face of Harrison Wells (Tom Cavanagh) in The Flash season 5 and season 6. Reverse-Flash returned as a major character in season 5 of The CW series when it was discovered that he was secretly helping Nora (Jessica Parker Kennedy) while imprisoned in the future. As it turned out, he was using her to plan his escape.
Then, Reverse-Flash returned in a big way in The Flash season 6 through one of the many changes made to the Arrowverse in Crisis on Infinite Earths. All versions of Harrison Wells merged into one, and for some reason, that included Reverse-Flash, possibly because he's still recognized as Earth-1's Harrison Wells. This merging allowed Reverse-Flash to possess the body of Nash Wells, but fortunately, Cisco (Carlos Valdes), Cecile (Danielle Nicolet), and Barry (Grant Gustin) were able to help Nash fight off Thawne. As a result, Reverse-Flash was "exorcised" from Nash's body, leaving him without a corporeal form. Reverse-Flash has been defeated, but The Flash has left the door open for his return.
Interestingly, the Reverse-Flash's many appearances across the last two seasons of The Flash haven't properly explained why the character still looks like Harrison Wells, which was his season 1 appearance. This has been confusing for fans, considering that the version of Reverse-Flash who stole Harrison Wells' identity was erased from the timeline. It would make sense for a restored Reverse-Flash to look like the original version of the character, as played by Matt Letscher. Matt Letscher played the villain in season 3 of Legends of Tomorrow and for a few episodes of The Flash. So why did the series go back to his season 1 roots? The Flash showrunner has explained that this particular version of Reverse-Flash seen in The Flash season 5 is the same version that crossed paths with Barry in the Arrowverse crossover event, Crisis on Earth-X (via EW) .
In Crisis On Earth-X, Tom Cavanagh's Reverse-Flash returned to battle the heroes of the Arrowverse on Earth-X. When Barry asks Thawne how he's still alive, Reverse-Flash responds, "With time travel, Barry, it's so very confusing". Apparently, this incarnation of the character is from another timeline, possibly one where he isn't erased. The Flash doesn't offer a more thorough explanation, but what they do suggest actually makes sense in the grand scheme of things.
Another factor could be Matt Letscher's availability. The actor could have been busy with Narcos: Mexico, whereas Tom Cavanagh is a series regular on The Flash, thus making it much simpler for The Flash to just have Cavanagh suit up as Reverse-Flash instead. Regardless of the reason, it's interesting to note that neither actor may play the villainous speedster if and when he comes back. And given that he's Flash's biggest enemy, it's less of a question of "if" and more of a question of "when". Since Thawne is without a body, he will have choose a new vessel to orchestrate his return to The Flash.