Its clear Cavanagh is having a blast playing this character and he's doing such a good job of making us hate yet like for him at the same time.
To be far the reason for their rivalries in the comics is rather weak and really revolves around Thawne having used his speed to change things in his past to better his future so much when he came to the present to meet Barry he became delusional that he was Barry, was rejected by the present as a suitable Flash and thus began their rivalry (with minor canon deviations over the years).
So any explanation for their rivalry in the show really doesn't have to do much to set itself apart. But its interesting that Eobaud is from a future less than 200 years in the future as in the comics he comes from the 25th Century which removes him a bit more from Eddy and better justifies the "distant relative" comment.
Given that briefer time divide and his comment to Eddy of being a genius even in his time I'm wondering if this Eobaud had actually started out good, using his genius to unlock the Speed Force to better society (much like his comments at the start of the season) but due to Barry running into the future following the Crisis his achievements were eclipsed by Barry already understanding the Speed Force and "stealing" his glory along with Barry continuing to be the Flash and a hero in that time. Thus began the rivalry over the slight Eobaud felt.
What's interesting about the "choice" is that even if Barry's mother lived it wouldn't effect with becoming the Flash because in the original timeline that happened cause the real Wells lived and built the particle accelerator which led to Barry's transformation. It just (supposedly) didn't happen as early so Barry was more mature and established in his life (possibly already married to Iris) by the time he became the Flash. However given the timeline of Arrow I'd think Barry transformed in 2014/2015 in the original timeline as well else he couldn't a critical strategic asset for Oliver to call upon as he was. So saving his mother wouldn't really change anything about his speed but more about how he lived his life and the confidence he had at the time of his transformation.
So the choice should really be about stopping Barry from ever going to the future, which could mean his death during the Crisis. So while he'd once again have a normal childhood with both his parents it would mean he dies in 2025 and thus allow Eobaud to control the future. So the real choice should be whether Barry would trade his future and the lives of the future for living a happier life up to 2025.
Making the choice to stop himself going into season 2 would make for an interesting story changes because it would keep Cavanagh in the show, as the real Wells, allow for the suit to undergo its minor changes to the brighter red and white emblem background and given Barry remembers his travels through time it would now be a mission of his "remaining years" to find a new way to survive the Crisis. Plus it would give us the chance to analyize episodes and spot tge differences in the timelines by giving the writers a chance to tweak some characters and plotlines that may not have turned out as expected or desired in hindsight. It also gives the show a good means to keep a villain speedster in the mix by having Eddy transform into Reverse Flash/Zoom either as a result of the time shift or, better yet, as a means for Eobaud to alter the past enough to try and ensure a better future for the Thawne line in the wake of Barry's decision by imbuing his line with the Speed Force earlier and letting it develop through successive generations (which could create a nice character arc for Eddy on whether he tries to team-up with Barry at first, thus why he takes the name Zoom, but is overshadowed by him in the public eye or if he's just straight bad from the go).
Just some thoughts and interesting plot changes that could take place if Barry went for a choice other than saving his mother.
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