it’s probably more that arcane S1 already premiered, and it’s not like they can (easily) go back and remake it to fit skarners lore. since they wrote the show to not fit skarners lore and be in some weird lore limbo (and have now changed it to be fully cannon) skarner and the brackern don’t entirely make sense.
You are correct in some regards. It was a couple of things. When we looked into it, what we didn't like about Skarner's lore is that he didn't really control his future and outcome. This really made him someone who was suffering an outcome rather than a main character with compelling goals that can be expanded upon, loved and empathized with. We don't want players to just feel sorry for the sad scorpion. But instead to understand his goals, his ideal outcomes and knows he has the power to potentially influence the political systems of a region. We also didn't want to completely take away the sense of loss of his beloved bond, so we thought the Ixtal people and the history he had seen can be part of that forlornness. His decisions has impact on the world versus being a victim. He is now in a position to decide, if he wants Ixtal to go down one path vs another. This also help build out Ixtal and the differing view points of some of the key players in that region. Previously, it was Qiyana and her imaginary friends :P (I see you reddit).
At the time, there were also higher level changes to the Lore where we were a bit uncertain the outcomes (One Runeterra was in discussion). We felt that we would be making players wait too long for the rework, if we waited for that discussion to settle. It would help us move forward faster if we build something compelling from scratch versus figuring every point of inconsistency in a changing dynamic of League lore. Especially in a world where synthetic hextech is the basis of Piltover.. it left not alot of breathing room for our beloved scorpion and his brackern (Why they killed them when they can just make it? Who found brackern crystals when Jayce and Viktor doing all that discovery? Etc etc). There were too many incompatible component that required us to withhold Skarner development. Mostly, during development we do DNA (Design, Narrative and Art) in parallel to make sure every element is cohesive. Narrative having to figure out the state of Piltover, Zaun and Brackern and make sure it retroactively in Arcane and other games in Runeterra universe is a huge undertaking in times of uncertainty. We prioritized getting him into players' hands faster with another compelling backstory than the original.