I've been playing currently a game with Patch III and I gotta say: superb!
I don't know what the german fans of PAE said (or is it personal choice of yours), but it is really true it is the most stable version by now.
For awhile, I felt PAE was pretty straightforward:
1) Steal some workers from AI (or if free worker from hut, let it be taken by the AI and retake it for slave)
2) Settle as Mine Slave
3) Great Engineer
?) ....
4) Profit
All games revolve with the strategy of settling most things in the capital and wait for Centralization civic to boost the unbalance even more.
In the end, the capital covered 80% of the economy.
For other cities, it was nearly no brainer field slaves and cottage everything.
Now, current choices are evidently chosen upon pondering the past situation. And bravo!
Because of you, I've got the Civ4 addiction nenewed. To think I was freed of it for about a year.
Now, the game is more tricky. War is also the same.
The idea of doubling most infantry movement points was a rebuttal to me until I saw the consequences:
Far far more dynamic wars. Plus, the constant typical let the AI slow army approach and bombard them with a shower of arrows to annihilitate them make the warfare redundant (despite it was still fun). That last situation is no more. The invasions are actually threatening now. Originally, even if my army was elsewhere, I stuck my finger into my nose and laugh seeing the enemy fell to my tiny defense. Now, I see AIs fall even on deity. It's on the good path because in Ancient Times, even the strongest could fall in a couple of years. For instance, the Assyrian empire was at its zenith during Assurbanipal reign to suffer a terrible fall following his death and ending so far within decades with the last king Assur-Uballit.
Originally, PAE was interesting mainly on the unit aspect given the extreme variety of actions not seen in other mods.
Economy-wise, the game has regained its strategic aspect. I've played various mods and one thing I've noticed is the no-brainer strategic paths.
The idea of allowing cottages by rivers/lakes and on hills is also a good way to remove the no brainer aspect of cottage everything. Adding hills is excellent because otherwise, the unbalance would have been terrible given those with rivers already huge advantage over others.
Interesting idea to add food consumption for Great Specialists. That helps in limiting the number of them in one city (although rare are the occurrences one will have enough of them to stiffle a capital food rate). However, one may inspect the AI reaction. I've noticed the AI seems reluctant to settle them. For some reason, I've seen AI cities with a bunch of them stacked (mainly Great Prophets and Great Generals). I am betting the ratio lost food vs gained commerce/science/etc. is not sufficient to favor settling. Hereunder I put a proof of that.
At last, it seems slavery pop rush has a nice ratio, making it efficient to do it. More than it was before. It's good because what adds strategic layers to a game is the number of degrees of liberty. For instance, one chooses things to build in a city and improve the whereabouts with workers. Both are independent yet linked. Two degrees of liberty. Cutting trees in the original game with efficient output is another degree of liberty. Pop rushes is another degree of liberty. War another.
Realism Invictus is another competing mod for, but they screwed it up when allowing K-mod to infiltrate. I like to play high levels, but already Emperor and their mod's games become unplayable if not slightly favored by decent lands and neighbours. Diplomatically, their design decisions made it a failure. A good mod, but some terrible design decisions (if options taken by default). It's all war all the time. Even your friends when left alone.
I play PAE on deity. It was mostly easy before and now, the challenge returned in force. And strategically, layers were added.
Big thumb up. The changes are major overhaul since the last updates. Also, nice new reskins.
I think at some point I should sign up to that german Civ4 forum to add my own spice.
I'd like to add this point again although this is a design choice you already justified before.
Libraries. I know you said some civs just burned them and didn't care of them. Plus, it was said it added different difficulty stages between the literate civs vs the non ones.
However, I think it is too radical to not allow them to at least capture them via technology capture.
For instance, Libyans captured Egypt diplomatically (Sheshonq, Osorkon, Tefnakht, etc.) and Egypt didn't fall into a dark age. When isolated, yes, it is normal they shall never learn about literature if historically true. However, it should be more flexible by allowing them through tech capture. 50% science difference plus the added perks with related wonders is way too much of a gap. Even the most barbarian civs know when it is advatageous to adapt to the conquered civ (i.e. Libyans, Mongols, etc.) Even about Nubians, it makes no sense they access as much as Egypt given it is because of the latter they became so literate.
I think more flexibility regarding certain tech capture would add a very interesting dimension to the game.