Projections is a perfectly good early Doctor episode. It walks so that later Doctor episodes can run and be even more amazing. For me, in re-watches particularly, it has at least one too many fake-out to make it really great (the false ending with Kes in sickbay). A few more on that list a really good too; it almost pained me to put Living Witness on there for example because I love it. I felt a little better about it when I went back and saw that almost all the TNG episodes that do fake-outs were good to great.
Voyager constantly uses the "everything goes back to the way it was" ending, but I didn't count all of them because they're mostly not designed to fool the viewers. Threshold is a fine example of that trope and a bad episode (though I softened to it a little bit listening to the Delta Flyers podcast; at least I get what they were going for now) so I'm right there with you on that one.
I like this theory in general and I think modern TV could benefit from more slower paced bottle shows. Maybe the fake-out is just an easy device to write within those constraints. But why does Voyager use it so much more than other Trek shows?