I think the geas, essences, and other stuff like that are a really cool concept, especially when it has far reaching, ions-old implications from long before and after they were first established in-universe. Cortana's plan is great because it would explain why she's always been a little bit special even with her unique birth. John is fantastic because it's just great dialogue.

I will agree with you that a lot of it is a little too neat and specific. The "seeds" to which the Librarian referred to are definitely one thing, and cool at that, but what they're going into is genetic engineering on a monumental scale. Forerunners were incredibly skilled at their particular craft, but they weren't the master manipulators of time, space, and life that the Precursors were. They're on an entirely different pillar of cosmic awesomeness that no one will soon achieve again.