I like the idea of the GP-only techs and wonders.. for the techs, you could do something like what Hydromancerx was suggesting for RoM's Civ V edition, with these "special" techs representing lost or alternate paths for history. For instance:
Prehistoric: Megafauna Domestication (Both potent and alternate history)
Ancient: Ancient Computing (The
Antikythera mechanism writ large: Big boosts to science output and the speed and power of all naval vessels right up to the atomic age. Also greatly speeds up calculation and computer-based technologies like Mathematics, Architecture, Computers, Radar etc.)
Classical: Greek Fire (Enables a new Fire Galley unit, ala Age of Empires, and a new Fire Tower building for the ultimate in pre-gunpowder defense.)
Medieval: Lost Relics (Enables the "discovery" of special items like the Ark of the Covenant, Shroud of Turin, etc. that act as world wonders with enormous benefits for particular religions. Would need at least one wonder for each religion of that time)
Renaissance: Da Vinci Tech (For lack of a better word. Early glider technology and aircraft in the Renaissance)
Industrial: Supertech (For lack of a better word, again. Think something like the early-Dreadnought that is
this monstrosity.
Modern: Ultraefficient Motor (Something akin to those urban legends about suppressed 200 MPG carburetors. A benefit akin to early Fusion or SMAC's Clean Reactors, with virtually no upkeep costs for engine-based units and greatly increased speed. Downside, of course, is that it would probably reduce the value of fossil fuels...)
Transhuman: Sapient AI (The potential for a global "robot rebellion", with a new faction, ala Planetfall's way of handling the SMAX factions, popping up and seceding from mankind, taking all the robotic units with it.).
Space: Time Travel (Dunno. Always difficult to use as a device without seeming contrived. Maybe some world wonder that enables you to recover any units lost in battle 10% of the time at the base the wonder is in?)
As for wonders, I very much like the idea of reducing the directly player-buildable wonders to ones that mostly just increase GP point output, and restricting things like the Sistine Chapel (largely the product of Michelangelo's vision) to GP's. You'd have to go through the list, of course, but the only other issue I can see you running into is that most "modern" wonders and projects (like the Manhattan Project, First Cloned Mammal, Cure for Cancer, Eden Project, etc.) have been "built" or will almost certainly be built collaboratively by groups of scientists working in tandem, rather than under the helm of a specific individual. Thus, most of the GP-wonders will be confined to the Renaissance.
Also, on a totally random note, I wonder what should be done with the "Civic" wonders like Women's Suffrage or Universal Healthcare. It doesn't really make sense to build these if you are running non-democratic politics or aren't using the Subsidized or Socialized Welfare civics. Perhaps remove the healthcare one and restrict Women's Suffrage to "democratic" forms of government (like Republic, Parliamentary, Federalism, etc.)
I'd suggest, if possible, to halve the bonus from retreat (+3 exp instead of +6) to reduce the speed at which warlord units gain experience a bit if dynamic XP is on. I'm happy to know you're going to cap out the withdraw to 95%, there should always be a failure chance. 
What if the Pyramids gave no 
