Brimstone's winrate is actually higher than Viper's across all MMR, with the exception of high elo (like, top 2%+), where Viper wins out. Good theory, just less focused on "Brim is better in low elos" and more like "Viper is good in the super high elos". It's also super close - I'd suspect Viper will probably overtake Brim in a patch or two as players master her kit even more.
Regarding Skye and Astra - I can give my take, but the best person to ask would be the head of the agent team, Riot MEMEMEMEME. For purely my opinion - Skye is inherently a very supportive agent who relies on teammates to extract a lot of value from her abilities, and Astra is a big-brain agent that scales on coordination, game knowledge, and creativity, so we've always expected them to be on the more niche end for agent picks - that's okay. We're always thinking about if there are ways to improve the experiences that we have on live, though, so that doesn't mean we wouldn't explore tweaking aspects of them in the future if we think it'd make them healthier or more fun to play.
edit: Edited my Brim/Viper comment above after refreshing the data from this AM