You make a good point and it's one that has not yet been considered.
The reason Theocracy was granted "Unlimited Priests" was because we were (or at leats I was) looking at changes that would open up a whole new early-game technological pathway (as mentioned before).
(This would enable players running a Priest specialist economy for a limited time).
If my suggested changes can be implemented and opens up a new way to approach the game I think that will be worth the negative consequence that you mention (that it's fairly easy (or much easier at least) to crank out a Priest for a shrine.) Either way I don't think it's gamebreaking, because Shrine's, although they can be fairly good, takes quite a bit of effort to actually become very strong and I doubt it ever wins you games. (Of course games vary wildly on different settings).
See below for my comments about increasing raw power against increasing opportunities to exploit the power that's already there.
It's not very effective early-game. In my Immortal games even getting a single religion does not always happen. Going for any of the early techs' that found a religion is rarely beneficial (never in my book).
The idea here was to make the Missionary an cost-effective alternative for building Monuments in new cities if you've gone the religious path early game.
If you can build missionaries, then autospread will quite probably take care of 95% of your border popping needs. Anyway, missionaries are indeed a troubling bunch. The way they are now they are very inefficient. In the current Taxman SG, we decided not to spread non-state religions we have a shrine for, because it's so inefficient. Lowering the absolute hammer cost is one way to attack this but as I said I have a feeling there's a better way

It's on the tip of my brain... Civic missionary build bonus is a good idea though.
This makes no sense to me, how is it any stronger than a Scientists with 3

(+3

running Representation)? If you're not looking to get a Great Prophet, why would you ever, EVER, run a 2

1

Priest instead of a Production tile (that also generates food) or spend that pop on a Cottage to grow it?
Of course you might be thinking later in the game than me, I rarely play the game past 250 turns...
Side Note: Engineer has been buffed to 3

. (which is better than 2

1

)
Simple. I'd run them when I want prod and am out of prod tiles. Happens often enough.
I'd be very wary of buffing the specialist yields - they can spiral out of control. WE/SSE is a tactic that's been proven to work up to & including Deity countless times, most famously by obsolete's series. If you buff spec yields, especially production, you basically promote wonderspam. This isn't necessarily a good thing and may not even fix the problem you want. And hells yeah 3

4

beats a scientist, hands down. Equivalent to 10

IMO. Engineers certainly wouldn't need the buff since GEs are so good, but it's not that influential since engi slots are hard to get for the most of the game and good for symmetry if the priest stats are changed.
Looking at the linked propositions, it would indeed make the religion game immensely more interesting. But there's waay too much power there. 4

/ 3

/ 3

from a normal damn specialist ('Mids repr, AW, DR) that plops out good GPs??? Holy CRAP, I'd just screw Education and go Rocketry and conquer the world with my unstoppable horde of zealot SAM Inf
AP cheese is cheese regardless of the relative strength of the Religious path.
Have you ever in a Immortal or Deity game gone for Polytheism->Monotheim->Theology->Divine Right tech's and been successful?
I'm not talking about AP cheese (doesn't exist in my world in any serious discussion about Civ4), and yeah, I've seen games like you mention, and tried some myself with varying degrees of success. Grashopa has some nice games in IUs for example demonstrating this (Imm/Deity). And there are tons and tons of games that heavily rely on UoS/SM/AP religion buildings for their midgame punch. However that's not necessarily what I'm talking about.
-----
Anyway. As a summary of the linked religion changes, I feel like you guys are
trying to give religion power it already has. It's just
hard to access. I'd attack that aspect more than the raw power, since just adding power leads to degenerate situations that don't promote play variety. Some aspects can use the power nudge as well but it's better for fine tuning IMO.
On high levels the most obvious problem of religion is that getting them yourself is a crapshoot. What usually leads to a more religiously oriented game is rushing a neighbor that founded one, this mitigates much of that problem. This means not pursuing Poly->Mono early. To get along in the religion gravy train, usually a prophet bulb or two is needed, which usually means SH or the Oracle (possibly captured as well). I see the religious tech path problem as being twofold:
1) Reliance on GPr bulbs, which relies on some early wonders if you can't get a religion (and thus run a priest). This could be attacked by making getting GPrs easier somehow (without temples!) - not sure how as there aren't any wonders you could feasibly "GPr'ize" on the non-religious tech path. I don't like the lenientness on giving priest slots to
everything, as I said IMO they
should be kinda hard to get if you're not trying. Giving stuff like ToA and Parthenon some Priest slots (probably 2) is one idea that pops in mind.
2) Exclusiveness of the religious tech path (key problem IMO). To go there you
must slog through the Poly->Mono->Theo crap. I see no reason why there couldn't be some changes in this. Maybe make Theology prerequisites (Writing AND (Monotheism OR Monarchy OR Code of Laws) (kinda makes sense), and maybe change DR as well (Theo AND Monarchy -> (Theo OR Philosophy) AND Monarchy or something). This combined with the GPr from DR would make it actually lucrative since SM is a great wonder if you get it running.
General note about testing. If you make changes and fire up the game in order to test those changes, it might be that
if they seem to work, they're too good. In a normal game, you don't start it with a certain tech path in mind, you choose it if it feels like the best choice among all. If it is always a viable choice, then there's a good chance it's overpowered.