The issue is, people who like the alternative seem to proselytize it.
There's nothing wrong with that, though. People who like a think talk about how the thing is good, and why.
Eberron's religion design is a lot more compatible with D&D, ironically, than 1E/2E's design. That's the key issue with Eberron. Eberron is a setting custom-designed to fit around D&D, specifically 3.XE. 1E and 2E had deeply confused and conflicting ideas about every single to do with deities/divinities. Nothing was consistent, nothing made sense, it was all clearly layers of whimsy from specific designers, many of whom, frankly, hadn't thought anything through, and were just spouting off half-formed thoughts as canon.
This becomes ultra-clear in 2E, with the various FR-centric god list books and Planescape, both of which work incredibly hard to try and square the circle of "How do gods work, actually?". Neither really succeeds, and a huge, huge problem is the repeated insistences from lazily-written power-trip-oriented* material for 1E where the gods definitely physically exist and definitely care about you, personally, mostly in a negative way. They also struggle with the fact that a lot of the gods from 1E have alignments which are wildly at odds with their actions/ethos. Even into 2E though you had designers randomly coming up with absolutely idiotic bollocks like the Wall of the Faithless (something Ed Greenwood has expressed his distaste for repeatedly, I note), which compounded these issues rather than helping with them.
And the amateur-hour approach is a huge problem, because it creates a situation that is both:
A) Incoherent, confusing, and obviously conflicted.
That doesn't work well when "gods are real and you can go bother them" is also true. If gods were just bad-tempered superheroes like in Greek Myth, it might work, but the confused and conflicting designer approaches mean most of them are trying to both be that, and to be some kind of Abrahamic god, and simultaneously trying to be some kind of "spirit of an idea", and it just doesn't work.
and
B) Not compelling or engaging.
Eberron chucked that all away and created a carefully-crafted set of religious/faiths that make sense, don't get in the way of adventuring, and allow for compelling intrigue, religious conflict and so on.
As others have noted, the faiths themselves aren't that amazing (they're not bad, but not amazing), but they're much better designed for D&D than the incoherent and contradictory mess that 1E/2E had. I say this as someone who owns pretty much every 1E/2E book that has anything to do with the gods, note, and who really has themselves tried to square the circle. The best you can do is ignore a lot of it and go with "Gods are just Tulpas".
* = Power-trip because either the DMs brought them in to "teach the PCs a lesson" with a being with completely OP stats, or the PCs killed them (like bedecked in Monty Haul'd magic items and level 30 or whatever) to prove how muy macho they were.
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