Finding the right mod is always going to be difficult. I can give you some general information about them, but you have to try them yourself, if you want to find the one most suited to you. Also, I'm not the best player (average at best), so I can't tell you which one is the hardest. We all try our best to make the AI better, but whose mod is the "best" or "hardest" is purely subjective.

First of all, you missed MarvinKosh's Space Weapons Fix Mod in your list. It is pretty much the inspiration for all the other mods. Well, except in my case. It only inspired me to expand my mod, but I was already working on it for a couple of years at that time. The only downside with MarvinKosh's mod is, that it isn't finished, because the tech trees of a couple of races haven't been adjusted yet. Even so, it should provide for an interesting play, because it is quite different from the vanilla game. The adjusted tech trees are much more optimised for the AI, and you have to follow a specific path to get to more advanced techs. You can't just go for the ultimate weapons, by going up the weapons tree in this mod. Early game is also much harder, as you have only a few Super Projects available to increase manufacturing and research. Factories and labs need to be researched first, before you can build them everywhere. This approach may not be for everyone, but it is quite effective at making the AI stronger. It's been awhile since I last played it, so I can't tell you how much custom content there is now, but tech trading shouldn't be much different from the standard game.

Tolmekian's mod was the second to be released and is much closer to the vanilla game when compared to MarvinKosh's mod, but still quite different. Among all the mods, Tolmekian's has probably the most custom content. New techs, new buildings, new weapons and defenses, new starbase modules, new icons and graphics for planetary improvements, new images for some races, etc. A lot of the existing techs and improvements have become more powerful. Weapons and defenses are also more streamlined (i.e., they are identical with each other except for damage type), but there are no ultimate versions, except if you go Evil (weapons) or Good (defenses). Tech trading, on the other hand, is impossible in this mod, because the AI will demand everything you got (at the least) for even the cheapest of techs.

Unlike all other mods, Autumn Twilight is probably the closest to vanilla TotA. I only rearranged some techs, removed a few others and added a handful of new ones. Some goes for planetary improvements and starbase modules. I also added a couple new invasion tactics (based on Mini-Soldiers) and flavour texts, but that is pretty much it regarding custom content. The rest is just editing what is there, so the AI has an easier time using it. Not much fun in playing, when only the human players can make use of most of the toys. Tech trading is still possible, but more limited. Almost all racial-specific techs cannot be traded or stolen. Same goes for all factory, lab, farming, economy and entertainment techs. Most of the other techs are freely tradeable, but I still need to adjust some of them, so they aren't too easy to get.

APT 1 is just a bug-fix mod, so it doesn't factor into this discussion. One of MabusAltarn's biggest changes in APT 2 is using the tech tree from DA as a template for all races. While that removes some of the uniqueness from the tech trees, it makes it much easier to adjust the AI. The different races still use their unique improvements, however, so it isn't completely the same for everyone. Custom content-wise, APT 2 is probably between mine and Tolmekian's mod. MabusAltarn added about as much new stuff as I did, if not more, but he also edited the UI in some cases. Tech trading is, with a few exceptions, about on par with the vanilla game.

As for compatibility with other mods, it depends. If the mod just adds new graphics, sounds or images, it shouldn't be a problem. However, if it edits the same files as the one your using, then it won't work. You would need to combine them, but that also means, that you have to choose between the changes both mods make. Not to mention, that it can take a lot of work.

Well, I hope that helped.

Twelve major race tech trees and one minor race tech tree, and one person to test how they perform against one another.

It's always going to be a work in progress without testers to feedback and say 'no no no these guys are way too overpowered now!'

That said I have been playing against and as some of the neglected races and I have preliminary fixes for the Krynn and some more improvements for the Arceans.

As far as difficulty goes, well the AI can put up a fairly good fight with any of the tech tree mods but ultimately the human player can win if the numbers and/or game position is in their favour.  All we can do is give the AI a shot at staying in the game.

As an example, one of the approaches I took to restructuring the tech trees was to have a central trunk.  This means that the AI cannot ignore improved research buildings and larger hulls.  This means that even in a time of war, it will in the long run balance improved weapons against more hitpoints and more research to get more weapons and hitpoints, either because it reaches the end of a weapon track or because it's the only reasonably-priced tech available.

I also cranked up the tech cost of fourth tier weapons and ultimate weapons so that third-tier weapons (including Evil alignment weapons) stay the most offensive weapons for a while.  This benefits both human and AI player by reducing the rate of escalation, allowing races to catch up and stay in the game.

I also re-costed a lot of weapons and added a new Omega beam weapon for those races which research Disruptors instead of Phasors.  I did this because in some cases you were actually better off skipping a tier of weapons and going straight for the gold; when you actually check the cost/damage ratio of Doom Ray against Disruptors IV, it's not terribly impressive as I recall.

And I added some new weapon sounds.  Trust me, the old ones were annoying.  Never mind that Laser animates three bursts per firing sequence and I have a continuous-sounding sfx, there were times I just wanted to get particle beams as soon as possible because the laser weapons didn't sound lasery enough.  If I knew how to fix the laser animation I would.