There are many issues with this great mod.
1. Withdraw chance
Already made a thread about it. Once you reach 100% (which is uber easy!), you can't lose the unit. It it has a small-to-none chance of victory, whenever it withdraws it will be considered as epic victory in the game, and the unit will receive max exp from battle (6). If you have leadership from warlord, it will get 12 exp for basically nothing that can be repeated every turn, leading to 200-300 exp in a VERY short time. While I loved the withdrawal feature, the fact it gave exp in vanilla BTS and always had a horse archer warlord with tactics+flanking to gain massive exp in every battle with minimum risk, +12 exp per withdraw is too much, and 100% chance of withdrawing is too powerful, especially with withdraw-on-defense feature because that essentialy is immortality.
The dynamic exp system was meant to prevent abuse, but actually it's WAY more abusive than the Vanilla BTS exp system. Maybe withdraw should grant a minimal bonus only? +0.25 exp and that's it? I find it hard to like that solution though, I would never reach the high tiers with my Warlord units if they were receiving +0.5 exp per battle... :/
I've conquered whole empires with two warlord units + great commander because they couldn't be killed, and with all heaing promotions AND medic they regenerated their health super fast. It was fun for the first time, but with third empire falling to two units, I got bored. What's the point of building units if you have immortal one that kills everything?
I suggest putting a global cap at withdraw chance at 90 or 95%. Reducing the bonuses to withdraw great commanders grant would also be fun. At fourth level all armies have +60% withdraw chance! Isn't this a bit too big? 10-20-30-40% would be already a huge bonus... Right now it takes any unit with withdraw chance AND access to flanking to immortality instantly. I recommend the numbers that the great commander grants to be greatly lowered - maybe even to 5-10-15-20? Or 10-15-20-25? +25% withdraw chance is a lot already with units that have access to flanking and natural withdraw chance, like all cavalry/helicopter units.
2. Upgrades of some buildings actually downgrade their usefulness
The most notorious example is Grocer and Supermarket. The Grocer adds +25%

and a LOT of

for access to certain resources. You lose ALL of that when "upgrading" to supermarket, and get what... a bit of

? Why would you want that?
Either the upgrades should carry out ALL of the replaced building's bonuses, or they shouldn't be replacing them!
3. Future tech upgrades not really well thought
A few complaints - The archer, riflemen, mech.infarty and all of that have one similar bonus - they are good at defending cities. And they get replaced by Tesla infantry that sucks against wheeled/tracked units (which will probably be your main enemy at that age) and helicopters (which are great units). The idea was that the archer line is good for defense, and tesla units are more of a offensive unit (100% collateral damage to 10 units!) rather than defensive. Which is weird.
Why can't plasma armors upgrade to Dreadnought Armor? Seeing that Drednaught armor has no drawbacks (compared to Plasma Armor) and should be a natural replacement...
Why isn't there a natural progression for artillery units? NLOS cannon is the last artillery unit. Sure, there are others doing collateral damage - like that siege droid with 170

- but why can't they be an upgrade? It's more logical than cavalry upgrading to tanks, anyway.
4. Religion bonuses not mutually exclusive
Why is it possible to take ALL the religion-based upgrades? Most of the time I just get all religions first then just convert to allow my warlord to get another bonus. Shouldn't it be like that: you pick one religion-based promotion, say crusader, and the rest becomes unavailable. Because the unit being a crusader and muslim's equivalent at the same TIME is pretty illogical.
Religion-granted wonders don't stop working when you convert! You only lose their

bonus, the rest remains. In a Islamic country, would you expect a wonder like King Richards Crusade to work? Not to mention that some are definitively bigger than others (see Buddhism wonders - Palace of Potala: +50%

, +20% :gold, +20%

stored after growth and +20%

, never becoming obsolete? That's like the best "commerce" wonder there is for a cottage economy! Compared to, say, Apadama Palace of Zoroastrianism.. lower maintenance and a free promotion? nice, but doesn't even compare.)
So, the player isn't rewarded for getting a religion... he's awarded for getting
all of them since he's pretty much the only one who can gain access to powerful wonders and promotions thanks to it...
It worked better in Vanilla Civ4: BTS, imho. I absolutely love the new bonuses of religions, but they ought to be mutually exclusive. (Afaik a wonder like Palace of Potala keeps working after you convert to a different religion, you just lose the "

bonus if Buddhism is state religion"... while logically it should cease giving bonuses)
So, a better balance of bonuses for religions and mutual exclusiveness of them would be a step in right direction.
5. Too much
,
and
The cities grow large even if poorly placed, the

is never an issue because there are millions of ways to increase

and each country is swimming in

even when REXing at 95%

rate. I literally swam in gold in this game. I expanded to 10 cities quickly and got +5

at 95% rate very early. When I turned it to 90%, I got +23

per turn! It's too easy to get rich, and REXing is not punished at all.
6. AI is still too weak...
Defends cities with 1-2 stacks, even Capital at wartime - BTS civ would have like 10 units there! Here I land on AI's territory, destroy 4 cities without any resistance, and reach capitol guarded by a single longbowman...
after 20 turns or so.
And it wasn't a pea-sized civ, it was 2nd Civ on the scoreboard!
Where's the resistance? I know my warlord unit would trample the down even if there was 10 longbowmen there, but the AI doesn't even
try.
There are many other issues but I think those should really be fixed soon

The mod has incredible potential... but is plagued by those problems right now.
Cheers!