In the defense of both Lost Frontier and Sly 4, they were both released on systems that were already near the end of their popularity while Ratchet and Clank released kinda early on the PS3 and PS4.
And both games were the worst in their series.
Releasing at the end of a gen should not be a huge detriment. You have a larger install base after all. The Last of Us launched just a few months before the PS4 came out. God of War II came out after the PS3 already released. I think what doomed those projects were they were spread across consoles and handhelds so they experienced less hype as exclusives . Also they both were poorly marketed.
Ratchet and Clank have had their misfires as well. Full Frontal Assault, Into the Nexus, not to mention a movie that bombed. I think Insomniac is just more passionate about that franchise than Naughty Dog or Sucker Punch were about Jak and Sly. We did not even get a new original Ratchet game this generation, we got an (awesome) remake/reimagining and it sold really well.
(Off Topic: I really wish they would add back online multiplayer to Ratchet. And to The Last of Us 2 for that matter.)