is it my imagination... or as the show progresses, does it seem to portray them more and more as "Prophets, who federation catalogs as "wormhole Aliens" because it wants to quantify, analyze and rationalize everything, and less "Wormhole aliens, who the quaint and superstitious bajoran's misinterpreted as prophets" Just it FEELS that way more and more as the series progresses.
Probably it does, yes, and that's probably because that's the way Sisko feels about them too. At the beginning he's respectful but still definitely only thinking of them in terms of the aliens he's used to dealing with as a member of Starfleet. By the end he's more used to thinking of them in a spiritual context - if not believing them to be gods himself, at least used to dealing with them in that way. Part of it may be just that he's surrounded by Bajorans always referring to them as the Prophets and a person just gets used to that, just like saying sidewalk instead of pavement or bathroom instead of toilet. And since Sisko is our primary Starfleet POV character in the show, it stands to reason that the show itself would begin to feel that way as well. IMO, natch. .
The Prophets also did more and more godly things by the end of the series, which could all both be explained by 'They are divine' or by 'They are 4d aliens who can see the future'. Both explanations are portrayed as correct and it seemed to come down to just whether you were a spiritual person or not.