Wrong game.
You are thinking of religion as a tool to power and more buttons to click. It was never intended to be that, and that's why you find it lacking. It's a roleplaying device. If you think of it as a gameplay mechanic, you will always be disappointed.
While I agree with you that religion should be a roleplaying device, some of the proposed measure are appropriate and would improve the link between RP and game mechanics effect. They're not power-gamey.
The tax proposal, in particular, sounds interesting to me. Right now, even in theocracies, all religions are taxed at the same rate. Allowing different levels of taxation would create a direct soft link between realm policy and religious spread which is currently often completely ignored. It would be historically accurate and create RPed interaction as realms would have a direct incentive to make their opinion of the different religions present on their lands known, rather than the ignore or destroy dichotomy which is often the norm.
