Ooh, good question! I think there are a couple answers for why the Princes appear less powerful in
Skyrim than they do in the other games, all more or less true depending on how you choose to look at it.
My first guess is that the Nords have always been rather distrustful of the Daedra. Their original pantheon is very Aedric, Shor, Kyne, Mara, Stuhn, Tsun, etc. all being explicitly pro-mortal and pro-Mundus deities, and with the adoption of their Imperial names and Cyrodilic orthopraxy I doubt much changed in this regard. Herma-Mora does figure in some ancient Atmoran myths as an enemy of Ysgramor, but his depiction as a crafty trickster is not exactly one meant to inspire admiration.
I also imagine that being surrounded by the Daedra (and later, ALMSIVI) worshipping Dunmer in the west, the Ayleids in the south and Reachmen in the east soured the Nords' perception of the Princes. They are foreign Gods worshiped by milk-drinkers and savages and not the honourable Gods that await true Nords in the mead-halls of Sovngarde!
Another factor, like you mentioned, is probably the Oblivion Crisis. The Nords already seem to have a cultural distrust of anything magical, and I imagine Daedric portals opening across the land would make local groups of Daedra-worshippers an easy target for mob justice, deservèd or not. Although unless I'm mistaken, Daedra worship was already outlawed under the Septim and perhaps Mede Empires. I think
ESO: Greymoor also explains how Meridia's temple on Mount Kilkreath fell into disrepair during the Second Era. And perhaps Princes like Mephala and Nocturnal simply like the shadows.
A final reason might be the nature of Akatosh/Martin's relationship with Nirn after their victory over Mehrunes Dagon at the Temple of the One. I think that they somehow replaced the Amulet of Kings and Dragonfires as the lynchpin for the barrier between Mundus and Oblivion, thus permanently shutting out Daedra without someone to conjure them. And you'd have to be either really desperate or really cocky to summon a Daedric Prince!
Anywho, sorry for the rather long response and welcome to the UESP forums