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There is finally somebody here on the forum that shares my opinion on how the transmission shifts.  I posted numerous complaints/concerns about this a while ago and what you describe doesn't seem to bother anybody else.  I can definitely feel a difference in how the truck shifts when it skips gears.  Unless you are getting on it, it will skip from 1st to 3rd by design and then skip from 3rd to 5th by design, but as you mention, those shifts take longer and are not as smooth as the other shifts.  I purchased an MPT tune to try and resolve that issue because their tune does not skip gears, but I am not completely satisfied with how their tune works because it holds, in my opinion, higher RPMs than necessary before upshifting.  The last time I checked with the dealer they have not released any updates to the shift logic, but if you find out something different, definitely let me know.  I am at the point where this is one of the last two things going on with the truck that keeps me from being completely satisfied.  The other issue is where the truck feels like it is missing on occasion.  I drove another Raptor and it did the same thing, so it may just be another quirk.