Okay so... I actually enjoyed the game that I played (am playing) but of course, time for negative feedback.
First, the latest version didn't seem to fix the city upgrades so it's a bit hard to discuss balancing issues, but there was one thing that really stood out, and that is the town's ability to produce troops faster than the fortress. I'm not going to get into the math here, I'm sure you can figure it out. The bottom line is that while there is a good chance you will build a town over a conclave as your first city, to get pioneers pumped out quicker, there is no chance you will build a fortress first. It is also questionable whether the fortress produced units are actually better.. In any case my suggestion is to have the fortress provide a 35% discount at the first level, in addition, or in leiu of the bonus level.
And on that topic, units need to be built faster. I've already had two computer empires eat the dirt becuase they couldn't keep up with the improved monster aggression. Build times for non-pioneer units should probably be 1/3 of what they are now, so you can either construct a building, a pioneer or a unit.
So the hero progression is a lot of fun, and was 1 billion times better than the random horsemanure stardock thinks is strategic... however there are a couple of issues with the level up screen. The biggest of these being, if you miss a class-relevant level up option you lose that option and all options associated with it forever. On these levels it should either be made clear to the player this will happen, or remove the other levelup options at important points.
Another issue with this, is that if a champion starts with a path before the ability to choose a path becomes available (I think some mage you save has this) he will have the option to choose a second path. When you consider that each path grants a bonus 5 hp per level, you should quickly put together how rediculous this becomes. Although I am -loving- the extra hp. No more 3 unlucky rolls killing my champions - yay.
The world monsters are probably a work in progress, but I thought it important to point out that the darkling and bandit spawns are both too frequent and provide too little xp for their difficulty. Also.. and amusing.. you accidently gave the epic dragon an attack rating of 14. I assume it was by accident seeing as the xp for the encounter was unchanged.
So... I noticed that new bows were available (I assume hero only) at the archery research tiers. Super awesome, except the same was not done for melee weapons. Work in progress? In any case the magic tech tree items are still totally borked. That is, the ignys longbow is at the end of the tree while the lightning hammer is at the beginning. Minor points.
Character creation is either bugged or intentionally made pointless. The soveriegn you can create only has 2 points available. That's enough to get a spell school and then summarily get thwomped. If it was a bug, I hope pointing it out helps you fix it. If it was intentional, then uhm.. don't. Restricting player options is almost never a positive route. Your base designs should be so good already that they beat the crap out of most custom designs.
And on that note, most of the changes to soveriegn professions were positive, but one in particular seems odd, and that is the summoner trait. It grants 4 extra custom points, but can be spent on anything. I presume the purpose was to allow the player to start with all spell schools.. Though why you would do this with the limited levels avialable is beyond me. In any case perhaps you could make it so that spell schools cost half as much, or grant an extra 4 free points to spend on spell schools, or perhaps you could forgoe the spell school benefits entirely and allow the sovereign to cast infinite summons at half maintenance. It's also pretty silly to give procipinee all the spell schools when her faction trait is to allow learning them with books.
Finally (yeah I'm all over the place here, sorry I'm tired!) altar's 20% experience bonus is not even worth a single level, since experience gains increase by 50% each time. In otherwords, this value needs to be at least 50% to provide more than a temporary advantage.