Here is a bit of information on a planned feature of the mod which will be implemented as soon as the advisor system is finished off. Yes, it's a completely new Religion system!
An all new replacement for the religion system (which I hope to carry over to Civ 5) the main difference is that religions are created by the player, as opposed to being strictly real-world religions, though each of the real world religions will be creatable using this system. The religion civic options will be removed and replaced with this system. Though all the effects from the religious civics will be available in some form in the new one.
Basically it revolves around a new religion screen very similar to the civics screen called Religious Doctrine.
Like civics, you will unlock new choices for your religious doctrine when new techs become available. Unlike civics, you can only choose these once and you're stuck with them for the rest of the game (though perhaps some wonder / advisor bonuses may allow single changes in rare circumstances). Some are a good way to get an early lead on your rivals, but have severe penalties later in the game (especially if you try and abandon them as your state religion) others will come later in the tech tree and provide later game bonuses but since you will have to reserve picking that category until they become available will mean you're falling behind earlier in the game. Some affect civs that have that religion in their cities, but not as their state religion negatively, causing unhappiness, unrest and other effects, making them a valuable tool for spreading and hampering rival civs. Some act like corporations, syphoning money, yields or resources from cities it has spread to, some have espionage benefits, and so on.
This will make the use of religion and the choices available a lot deeper. Your religion could be tailored to war, being able to create 'crusader' units (any unit type) that both spread religion and gain bonuses against the heathens, others built around philosophy, providing scientific benefits but being extremely unprepared for conflict. Others may be focused on economy, making citizens happier, more subdued or more productive, keeping citizens in line and quelling discontent.
You will find religion has a lot more potential to force your hand, with the religious leaders having varying levels of control over governmental affairs depending on the religious doctrine options.
As well as this, Atheism will be a new 'religion' which will be automatically founded in the civ that first gets advisor Charles Darwin settle in one of their cities. Atheism then spreads as would a religion, which provides benefits to science but can seriously damage a religious leader's civ if they do not manage to control it. Some religious doctrines will be accepting of atheism, and for some it will rip the civ apart with unrest, others will simply reject it.
Another major change will be that religion will be specific to population, not a city wide thing. If a city has 12 population and you found a religion in that city, only a few of the population will be of this faith. This will grow, and when other religions attempt to spread there, it will only happen if there are either populations who haven't yet adopted a faith (religious doctrine will determine how likely new population are indoctrinated into the state religion, or left to make their own decisions), or how open the existing religion in that city is to conversions. Some of the more fundamentalist choices would mean it was practically impossible to spread your religion there. This will basically replace the Theocracy civic choice. But then if you can get immigrants to move to that city, it is a way to spread your religion there. However when the whip is used to rush build, it will always choose non state religion population and immigrants first (though the latter could potentially cause diplomatic penalties in the rival civ) since the religion is tied to the population and not the city, this means it is feasible to remove religions from cities through more morally dubious means of population control.