Some general comments and observations
I normally play super huge custom smart maps, at snail/deity w/ 24-32 starting civs.
My last game was v1.55
Bandit/Merc units needs to be excluded from the set of free units that a Barb city turned minor city get for free. They end up crippling their income.
If the Apiary ends up re-obtaining a honey resource, I'd restrict it's bulidable location to only those cities which have a plant based resource which insect dependent flowing within its city cross. (Apples, Lemons, Wine/Grapes, Cotton, Spices) Note that I don't mean these resources should be required (be linked up) to build the building, only that the are visible and within range.
Fixed borders: Interesting concept but the AI just can't handle it, I know this has been mentioned before. I support the idea of not allowing claiming on ocean tiles, which I read in some other place somewhere. I also say that one should not be allowed to claim territory that is more than X distance from your nearest city (possible the max culture distance.) Even at deity level (which is way too easy but I'll get to that in a bit) I could beeline democracy.
Ritualism->Mysticism->Priesthood->Writing->Alphabet->Democracy (popped w/ oracle)
Once obtained I switch to get fixed border and use claim territory to literally box in all my neighbors prior to 1000 BC. Even though those spots are far far away form my main cities and I don't leave units on them. Claim territory has the added benefit of displacing fog of war. No FOG no Barbarian spawns. Before I'd just set up units to do this, now I don't need to keep a unit dedicated to it. Also there is definitely a bug in the contested territory squares. It seems that if you tie the the number of controlled tiles surrounding an unclaimed tile, against a neighbor, the player always wins the content. Even if each side only had 3 tiles bordering the unclaimed tile. You should skip trying to to a compare againt a rivals tile at all. Make it simpler, so that you can only gain a tile if you have control 5 or more of its adjacent tiles.
Teching is slow, but its still too easy to beeline for players. (since they AI currently can't do it very well.) I propose putting in place (or increasing it if it already exists) a cumulative penalty when researching a tech for each tech in an era prior to the era of the one being researched, that the player does not have.
Tech leak rate from master to vassal should be doubled.
Key techs should increase the amount of tech leak their owning civs contribute to the overall global effect. These techs should be commutation related techs (writing, alphabet, paper, mass media, etc)
I like the ideas of converting most of the % bonuses to static bonuses as well, as mentioned elsewhere.
Having pyramids give free irrigation canals doesn't make sense to me. For a free building I'd suggest something more Tomblike, perhaps graveyards, but I don't even like building graveyards, their benefit is not worth their maintenance cost. Maybe ceremonial altar instead.
I personally always tweak the resources xml file. I make all mineral based resources capable of appearing in almost any terrain (the only one I sometimes disallow is marsh), with a non-grouping random distribution more like that of the standard iron/copper distribution. All plant and animal based resources I set as area/continent based (with the exception of horses) I get a much better distribution and almost never have missing resource problems.
I also always remove the fresh water flag from Jungles. This is possibly one of the reasons (certainly not the only reason) that AIs have bad city placement. If they are doing fresh water search checks, then any jungle qualifies.
I usually allow oasis to have improvements built in them, it helps the nearby city, (player and AI) which may already suffer from a glut of desert tiles.
I think that the resource granting quantity of a lot of the national wonders should be toned down, such as the brewery giving 7 alcohol instead of 9.
The Shewdagon Paya (or whatever the wonder it is that grants all religion civics) need to be given some other ability, unlocking all civics in a category too powerful in RoM)
As someone mentioned elsewhere, I like the idea of allowing hemp to give a production boost to wooden ships, probably via the shipyard, cotton could as well.
As many others have mentioned the AI needs some serious improvements. This deserves its own post though, as other have already started.