This is interesting... I feel like more often I run into games that have a great premise with holistically poor execution, rather than a poor showing in general with one standout mechanic (or maybe those just don't stand out as much in retrospect). But there are two that I do recall:
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I found Brothers: A Tale of Two Sons to be largely schmaltzy nothing with an overly cute control scheme but there's a moment at the very end where the controls pay off magnificently.
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I think Cultist Simulator's core simulation of story through cards is excellent and gets completely squandered by the absolute nothingness of its progression (also iirc the creator is a shit).
