Exactly, Kizuya-- I couldn't agree more and I'm really glad to know many more people gravitate to the incredulous way both of them were discarded. Back then, many of us had really great discussions on discord about the missed opportunity with these characters.
Also... (lots to read here-- the words just kept coming as I kept editing)...
I was seriously hoping that the Devs would expatiate a LOT more about their story through our echo ability-- their childhood, their friendship, their ambitions to clean house, Regulas' restructuring of the corrupted VIth legion when he took over, the machinations against him at the imperial court and how Varis staunchly supported him. I really, really liked their story and wished we had delved into it more.
All these would have been fantastic side quests we would have explored extensively whenever we made it to Garlemald. When Gaius re-appeared in patch 4.X, I was super excited not only because he had been one of my fav NPCs from the very beginning but also because his return and subsequent interaction with Varis would have been perfect for our echo ability to discover the Garlean past. We could have used the echo to further understand the narrative of the Empire's past, the genesis of Emet's reign, the political agendas of the earlier generations of the imperial family, the identities of the nine aspirants to the throne -- all through the eyes both Gaius and Varis. In other words, Varis would have shown us the inner happenings within the royal family-- Gaius and Regula would have shown us the happenstances around the royal family and the empire.
(cut because character limit)