This is only my opinion, but I feel that supernatural powers should be far more common amoungst members of the big factions.
This is only my opinion, but I feel that supernatural powers should be far more common amoungst members of the big factions - Guilds, Houses, Church than with the majority of the population and these groups should also be able to develop a characters abilities in a limited way. It explains the number of PC and major NPC psychics, if nothing else.
However, the process of switching on Psi or Theurgy shouldn't be entirely under their control or it would be done even more often. Getting high level powers should mean going outside these organisations and the PC should either have to do something to himself or get the help of some supernatural force.
Theurgy is probably a mix of faith and lengthy study, so that its possible to get so far (Theurgy 4 or 5 ?) with just an average amount of faith and good teaching or lots of devotion with just a little learning. Beyond that point it takes hard work to purify the soul and grasp the deeper meanings or principles behind the doctrines, understanding is more important than rote, restricting the greatest powers to a handful of priests who are often in the worst places, where they are most needed.
This allows lots of folks to have low levels of Theurgy: saintly peasants (watch out for the Inquisition !), Adamantine knights and young noble priests, who may be worldly but spend a long time in training. Bishops are capable people but are not necessarily devout and have to spend their time on politics so rarely get past non-specialist level. With spiritual and political power split between very different people all kinds of problems can arise...
I've thought a fair bit about FS occult stuff (and even thought about re-doing the system) and have several reasons/plot hooks to explain the distribution of supernatural power:
1) Artificial evolution. Genetic engineering and the use of symbiotic nanites may have been far more common than Church histories admit. This kind of thing would have been concentrated on the rich and the effects could easily have run out of control. So their descendents unwittingly benefit from it, but trying telling a noble bishop that his knack for Theurgy comes from 2nd Rep nanites that he caught from a treasured heirloom or in utero from his mother !
2) The jumpgates, of course. Every human in FS has at the very least one ancestor who went through one jumpgate, and most have lots of jumps in the family history if one goes back far enough. This isn't always true of aliens, and may partly explain the lack of psi in some races. Guildsmen, nobles etc. travel a lot more so get more exposure. There is no guarentee that human-made Sathra dampers are actually 100% effective, passangers just don't _feel_ anything odd.
3) "Psycho-social engineering". 2nd Rep techniques to alter human behaviour and maximise human abilities may be a widespread part of professional training, though they have often devolved into ritual and mysticism. Since the Church prefers right-thinking people to machines it may actually make more use of training to be able to handle record-keeping, navigation and higher mathematics with the minimum use of soulless contraptions.
The nobles also look like prime users of psychology and mind-bending techniques, not only on their retainers but also on themselves. Why do nobles of each House have similar personality traits and display advanced skills at a young age (a twelve year-old Hazat leading troops) ? Maybe because they are rather efficiently brought up that way. Ditto with the Guilds. Tuning peoples mind-sets at a young age may produce unexpected results.
Obun society could be intended to minimise the problems with Urge and having large numbers of mind-readers and potential mind-controllers. The Obun might even keep order through mind-control or a hive-mind effect, it would make them seem less damn nice anyway. This continual exposure to psi may activate the talent.
4) Supernatural entities. If these have any existance outside the minds of individuals, perhaps living in the Universal Unconscious, they probably have more contact with the nobility, the Church and the Guilds than anyone else since these are the people with power. They are also the people with high-tech. I imagine that the Phavian Institute had far more effective devices than ouiji boards.
5) Phavian and Ur tech. All the Known Worlds have been affected the Ur, whose devices may have included devices to focus or channel psi power on both small and large scales. Psi or Thurgy may be the ability to tap into a planets Ur psi-network, which in turn taps the minds of sentient inhabitants. Whatever the Ur left behind is in the hands of the three powers, to use and abuse to the limit of their understanding. Taking holy orders may only occur in certain places or in the presence of certain objects.
Ratios of psychics or theurges to non-psi seem to be very variable and completely subjective. In the books nobles seem to have more psychics than the Guilds, and all the priestly characters have Theurgy. How common psi is amoung the nobility depends on how many nobles you think there should be, my feeling is that there is a high proportion of potential psychics (maybe 1 in 20) but it takes an exceptional character to jump to full Psi status, hence many top nobles like Salandra Decados have some powers. For ordinary people it may be 1 in 20,000, enough for the supernatural to have a foothold everywhere, but very, very few develop powers and stigmas without outside intervention. Theurgy and Antinomy may be available to anyone who develops their faith or their knowledge.