If you're looking for one that doesn't do this, I recommend one of my favorites, "Tsuki ga Michibiku Isekai". It starts off seemingly generic with the usual small twist that the protagonist has god-like powers right at the start rather than having to work his way up to it by defeating the armies of the demon lord, but spirals into an absolutely fascinating Intrigue plotline concerning the protagonist's origin, the nature of his powers, and what the isekai world really is. It constantly made me question what was really going on, and more than that, it suggested that there was some real gravity behind all of it. Even side storylines like with the Rembrandt company end up with an impressive amount of depth, secrecy, and intrigue, with really compelling character development. I can't recommend it enough.
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