I think we don't have enough elements to compare the two approaches properly yet. Some of Amagami's flaws could be attributed to the directing (or even the original material) rather than the format of the story. I have a feeling Yosuga no Sora will handle the omnibus format better. For one, having common episodes for some of the heroines is definitely a good idea.
I honestly can't say which approach I prefer right now. Both can be valid options depending on the original material. Amagami's plot relies heavily on the romance aspect and thus is better suited for omnibus.
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