Reckoning's failure stems from not having a firm vision of what it wants to be, or not letting someone with a firm vision of what it should be in charge of everyone working on it. Every flaw you relate - and they are real, genuine flaws with the product - stem from the game trying to be A, but also !A.
Personally, I like the Messengers being vague, untrustworthy sources of power who make a vague offer, give you powers, and then generally fuck off without giving you an idea of who or what you are in a world that is now much scarier by a factor of a billion. Some groups in Vigil use this same premise to a greater or lesser degree - the smaller, mid-tier ones mainly, but I think there's an argument to be made that Cheiron and the Lucifuge are what we could have with more hands-on Messengers.
Mercy is definitely weird, but I think that there's a place for the premise, if not the implementation. Because basically every splat started out as a normie. So there's room for peace and co-existence and un-monstering monsters. That kind of thing can fit into the premise/theme 'Inherit the Earth.' The actual Innocent Creed as written? Not so much. That's maybe a relic of WW design where there has to be designated pacifist fucktards, a la Children of Gaia.
Vigil is definitely better at what it does, but I don't think it was trying to be a fix for Reckoning. It was more an update to earlier Hunters Hunted types, I think. Probably better for it, rather than trying to re-work Reckoning.