Yes. These problems were pretty evident in the core set meta, but the first cycle has allowed people to make much more effective and consistent decks across all factions, and more theory/deckbuilding time has led people to cheaper cost curves that give more reliable command starts.
Space Marines are certainly good but not dominant, and as player skill increased cards like Doom became much less relevant. Doom is in fact frequently omitted even from decks that can take it, and is usually only a 1x in those that decide to keep it. Exterminatus (another early problem card) is almost never played anymore.
Cato is strong but nowhere near as strong as he once was. He’s probably still in the top tier, but he has a lot more competition. Even among Space Marine decks, there’s a big debate as to whether Cato or Ragnar is better, and Space Marines are no longer the clear best faction. The “top tier” warlords right now are Cato, Ragnar, Kith, Eldorath, and Zarathur, with Coteaz, Baharroth, and Aun’shi close behind. Of those, I think Cato is probably the worst right now.
My main interest in Netrunner is to scratch my cyberpunk itch, but there are still a bunch of things that bug me about it. I’m much more confident in the design and direction of Conquest and I think it will almost certainly remain my “main game”. IMO the first cycle in Netrunner basically failed to hit several key objectives, while the first cycle in Conquest has been pretty awesome, and the upcoming Tyranids look to provide some really interesting new shifts to the meta.
Overall, I like the symmetry of Conquest, prefer only having to build one deck instead of two, and I think Conquest weights success more heavily towards play skill rather than deckbuilding skill when compared to Netrunner.
That said, Netrunner is also an awesome game, and I look forward to having the best of both worlds!