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I like the idea of the Sith being in hiding and by the time the Jedi start suspecting them, it's too late for them to do anything about it. It just seems very Sith-like to me. It's what the Banite Sith did after all. Life, I think you're right that a technical reading of Legacy, leaves the door open to the Sith revealing themselves during the FotJ era, but I always got the sense that the Sith would remain in hiding for far longer.
While I'm not a fan of the Legacy comics I liked that aspect of it. Personally, I would actually be happy if the Legacy comics become non-canon, but there are some things I would like them to keep (Sith in hiding, Fel Empire etc.).
Where sky and water meet,
Where the waves grow sweet,
Doubt not, Reepicheep,
To find all you seek,
There is the utter east.