I do understand that the hardest part of developing a game like this is balancing. It makes herding cats look easy!!! And I understand that the developers have their vision of this game and that's what they are going to develop. BUTTT... here are my thoughts if anyone is interested.
I like heroes being powerful! They're supposed to be! But I don't like trained units being totally useless either. And it takes so LONG to get techs to build units that are useful (and then actually BUILD those units) that I'd be bored out of my mind if I had to wait until I could build decent units to fight some of the mega mobs out there. Moving Leather Armor closer to the start of the tech tree helps some. But I think a better selection of low-level "Crude" weapons available either at the very start or quickly researched might help. Techs researched can then provide upgrades. In my perfect "Fallen Enchantment" world, every Army would be composed of approximately 1/3 to 1/2 heroes and balance trained units. And it should be nearly a requirement that every army have a mage or at least an archer or two to deal with enemy mages. Of course, I know that's MY vision and not necessarily Stardock's vision.
I also tend to agree that the combined build queue also discourages building trained units. I have to say, I'm not sure I understand the argument against having two different queues. Allowing the building of lots of trained units (as cannon fodder if nothing else) would encourage opponents to do the same. Make them easy to build and then use maintenance cost as an easy way to control the numbers.
The problem with slowing down the leveling of heroes to me is that then suddenly, you're surrounded by monsters you can't defeat and you're stuck clicking the "Turn" button waiting on trained units powerful enough to help to be researched and then built. In the earlier beta, I had that happen to me several times and it's frustrating. The solution to that would be increasing the map size but right now the game isn't balanced well for larger maps (OP heroes is even worse!) and there is the memory problems. As it stands now, I don't think that map size balances well and probably never will until XP is controlled by map size.
I don't dislike having heroes more powerful than units. I think they should be. But I don't think a small group of two or three heroes should be able to steamroll everything it its path. The ideal situation would be to have types of units that are especially effective against heroes but I can't think of any way to implement that at present. Shrink works pretty well against large, single monsters and could work well against melee type heroes but it is really easy to resist. I would fix shrink so it is harder to resist for heroes.
An option for dealing with mages might be a "Silence" spell that prevents (at least for a few turns) a mage from casting any spells. But, as a pairing to that, you would need a "Remove Enchantment" spell that would allow removal of such spells including Shrink and Silence. The net effect could be that mages become as much or even more defensive rather than pure offense. It may also force players to cultivate spellcasting more in heroes and space them out more. The effect being a city without a spellcaster could be a sitting duck.
Another option would be to restrict spellcasters to not be able to wear armor (or perhaps metal armor) or use a shield and tune the AI to target mages and sovereigns. This forces mages to be we well protected and vulnerable. It also forces players to choose whether their heroes will be mages or melee. One game mechanic I really liked in WoM was the Imbue Heroe for this reason. But I do think that the "Paths" mechanic makes up for that. But I think the wearing of armor and the use of certain weapons should be a trait gained through a Path and not something that every hero can do. I also think that once a Path is chosen, no other Path can be chosen.
I think it would also help if Army size is increased. Right now I have no trouble filling out the ranks of my pitiful 4 or 5 unit armies and getting beyond that takes too much research time. And having larger armies of monsters with cannon fodder encourages more cannon fodder.
Some sort of artificial "aggro" might be useful for trained units to allow them to protect heroes. This might also give them some usefulness particularly in protecting more vulnerable mages. This makes archer units natural mage killers. To balance archers, shields should give a HUGE "dodge against ranged" bonus (and guess what, mages can't carry shields) so that melee units are protected against archers.
Right now, I think the mana balance is better but a bit stingy. Mages should need to sit out of smaller fights to conserve mana but be crucial for bigger fights. It should be difficult to defeat larger mobs or opposing heroes without a mage. It should also be a big disadvantage to go against a mage without a mage. Mana availability is a good way to regulate this by preventing a mage from being able to blaze through all the fights. But how do you balance this with monsters? Perhaps higher level monsters should either be mages (like elementals) or perhaps have some buffs requiring debuffs. Not sure without thinking about it.
Anyway, this is my amateur Game Designing thoughts. Flame me if you want. I don't really care.
