I agree with you on everything except for religion. The Civilopedia is hideous, not at all easy to navigate and just not high quality. The Civ 3 one was near perfect. The science advisor isn't absolutely horrible like the Civilopedia, but it still could use a major overhaul. Those pictures of units, not the names, almost ruin the game. In Civ 3 you saw the full picture of the unit, not a headshot, the full graphic though minimized, and the unit/tech/whatever's name. The Civ 4 interface makes too much use of small windows and as few words as possible.
This mouse-over stuff is also really annoying. Posting screenies of the game, I noticed that when I minimize the Civ 4 window by bringing up the start menu, if you leave any screen within the game open, you can't play any more. For example, I took a pic of diplomacy with Huayna Capac. When I brought the window back up, the "Farewell... (EXIT)" option is blocked by a transparent layer of the RTS-style interface. I couldn't even re-start the game, I had to load from the last save. The Civ 3 interface was beautiful and very well-conceived. I never liked RTS-style interfaces much, but Civ 4 really brings it down to another level of dissapointment. Remember the espionage screen in vanilla Civ 3? In Civ 3 PTW it was overhauled to a very beautiful screen with all the civ leaderheads and diplomatic or spy options right there. Civ 4 needs a massive interface overhaul for the next XP.
And my main gripe is modding the game. This "powerful" world builder has some nice features, but it suffers the same interface problems as the main game and you can't change the rules! I complained a lot about the Civ 3 scenario editor, but it is far superior to the Civ 4 one, except for being accessible in the main game, that's nice. I want a scenario editor in which you can change the rules and add civilopedia entries. A true modding program with a finely-tuned GUI.
Civ 4 is definitely a step in the right direction, for the most part. However, it is not remotely as playable. When I first got Civ 3, I was hooked from the beginning. Civ 4 I was excited for, but it's just an obnoxious failure after too long. Or maybe I'm just cranky from hours of gameplay.

Also, it does suffer some features problems. The tech tree is disjointed, you go through phases in which all you hear is Leonard Nemoy's voice, the game isn't changed at all. Then the game is turned on its head. A more steady progression (but of course with periods in which things don't advance as much and also some more technological booms, but still consistent) is sorely needed. I am just whining now, I don't really hate the game this much. However, if I wasn't such a sap and hopeful for an improving XP, I would return it.
Sorry, Firaxis, you really dropped the ball on this one. Many good core elements, religion and such, but poorly executed.
