Willowhaunt said:
To build a world, to run an intrigue/secrecy/political campaign, or to make the game fun for everyone involved at every level of play, that's what I'm worried about.
Sorry this is so long, but your real question is about how to set up a DnD campaign the way you want it. It's a really complicated situation, so I don't know how to do justice to the topic without a long post:
MAGIC IS IMPORTANT
IMO the first thing you have to do is accept that magic plays an important role in a DnD society. It's not all that different from actual historical societies that believed that the gods or whatever had to be on their side for them to be successful. All viable groups of persons are going to have important persons within them that have spell-casting capabilities of some kind. This could be a cleric-chaplain, household bard, or court wizard. Even low-level spell caster cohorts of a high level fighter can significantly augment the power of a high level fighter by covering for some of his weaknesses. This doesn't mean that fighters don't rule. But it probably means that a fighter without some magical resources cannot (depending on the size of his domain).
LEADERSHIP IS NOT ABOUT WHO CAN KILL MORE THINGS AS AN INDIVIDUAL
Leadership is about who controls the most powerful resources in the kingdom/society. A pair of 10th level wizards might find it in their interest to follow a 20th level fighter, and kill a rival 20th level wizard. The fighter provides them with the security of a front-rank character that they know won't teleport away on them at the last minute. True, the fighter, winds up with more killing power but it's not because of his personal capabilities. IMO fighters make better leaders than wizards because they lead by example.
DEMOGRAPHICS IS YOUR FRIEND
You have to consider demographics - and I don't follow 3E on this so I'm not sure if this is cannon. But in general - a high level wizard SHOULD be able to dominate a village. What happens though, when a 15th level wizard not only has to contend with a 15th level fighter ruler, but also a host of 10th level characters of all classes who each serve that 15th level fighter in some capacity (guilds, vassals, relatives, former adventuring buddies, cohorts, etc.) It's not as simple as just bumping off the 15th level fighter and thinking everyone is going to love you for it.
Also - demographics can be your friend if 50% of your world's population is not a 20th level character. High level characters who are rare enough would control large portions of the population. Even with 10 times as much divination and scrying, there's just no way to keep track of everyone. An evil wizard would spend his time scrying a pair of whispering lords at court, only to find out they were gossiping about an affair, while a real assassin took advantage of the wizard's distraction to plot the wizard's death. And consider that a number of mundane protections (like lead-shielded rooms) might be in common use in the society, similar to the various superstitions (throwing salt over your shoulder to ward off curses) in the real world.
THINK OUTSIDE THE BOX OF TYPICAL DUNGEON CRAWLING
For example - there's no reason that the gods would not notice the death of even the least significant of commoners and decided to send down a deva, pack of blink dogs, or whatever, at a critical time to counter the schemes of the Evil Wizard trying to dominate the world. Even simple advice provided by an incorporeal spirit to a group of vengeful fighters ("here's where the wizard teleported to") can really tip the scales. IMO the slaying of a high level wizard in this situation would almost require a few special events. Also consider that every high level character in any given world is not accounted for. High level characters could be retired and operating as bar-keeps or whatever. A commoner runs into his bar, and he decides to get the old group together one last time to go kill the Evil Wizard usurper.
SPELLS HAVE WEAKNESSES
Detect thoughts only works when the person knows they're lieing. If I'm an 8th level fighter vassal to a high level evil wizard, you better believe I'm going to avoid meeting with him at all costs. I'll send my seneschal, who doesn't know he's lieing. Or I'll buy a Ring of Mind Shielding.
Sense Motive reveals a charmed/dominated person IIRC.
In addition - I think you are completely justified with developing spells to counter some of the high level spells of 3E because I think the game does a good enough job with providing counter spells for the lower level ones (see invisible, misdirection etc.) but tends to fall short of the higher level ones. For example - a Glyph of Warding that goes off on anyone that teleports into the area. Spells that feeblemind the first person who scrys into an area.
THE FOG OF WAR
Take all of these issues together. Take the situation of characters switching allegiances, of family and guild ties, etc. The hypothetical wizard who you think is going to rule the world is going to have to watch his back constantly. Even a simple misdirection spell might mean that he attacks the wrong person at the wrong time. IMO there's just too much going on, even in a magical world, for any one individual to dominate a situation without the same leadership, organization skills, and perception and real world leadership requires. And IMO the spells don't help you with that, and I would think each class would have it's share of persons gifted in those areas.