First of all after playing through several times .86 strikes me as the beginnings of a great game. Way to go Stardock. However since criticism is what will make this game better here is mine. The strongest part of the game right now is the questing and magic. It's just fun to explore the interesting worlds that you have created. Also magic is fun and interesting as well. Not that these areas are perfect, far from it, it's just that they are the more fun areas of the game. As the downside city building and research are very boring. The order of some of the techs is kinda weird, and cities don't really need to specialize at all so they all feel the same.
The new focus on crystals, capital, and metal is awesome and adds depth but currently is underused because it is unbalanced.
Reduce the amount of crystals, scenic views, and mines on the map. Also halve the amount of resources they produce. You get too much of them. Instead add some more buildings to cities that multiply their production. If you want a lot of metal you should have to specialize a city around it, same for crystal and capital. This way every city will be different and which resources you control will help you decide which techs to get and units to build. You also won't need every resource every game, scarcity will just encourage different play styles. Scarcity will also make some other buildings like armorers more useful. To a lesser degree this applies to even horses. If you only have one horse tile but want to build lots of horsemen you should be able to build some buildings that boost your horse production.
The same thing applies to mana. Currently it requires no planning to rack up ridiculous amounts of mana. Reduce the amount of mana initially generated by shards to 1. Then add buildings that boost the mana produced by shards in a city. Techs on the magic tree could also boost mana. Right now mana just builds up in the background, while it should be possible to get a huge mana pool it should also require some active participation from the user. Nothing too hard but building up mana should be a strategy not a freebie.
Reducing the base amount of resources produced and requiring cities to specialize towards these resources by building specific improvements will make cities stand out and be a lot less generic. Also requiring a little more planning to maximize resources and requiring players to develop their long term strategies around what resources they have available will help draw people into city building.
The research techs are placed weirdly. There is a big gap in the research techs after education, this slows research down midgame because you have increasing costs of research but no way to increase your research for 2-3 tech levels.
I won several games through conquest and magic but never got Higher Education. Why is a research tech which is only useful in order to get more research basically the last tech you get? That makes no sense. Also since war colleges require it it makes pikes almost impossible to get as well. Higher education should really be earlier on the tech tree. I was running around with champion armor but not pikes because Higher Education was so ridiculous to get.
Since Civics research is the only way to increase your ability to get any type of tech it forces everyone to mainly use civics techs and only worry about military and magic as a side issue. To make magic tech more interesting you should add a tier 3-4 research building. That way there is more incentive to actually specialize in magic instead always going civics.
Change barracks so they reduce the upkeep of stationed units. That way players who specialize in military actually get some bonuses and can afford a army without relying on civics completely. If you look at the honor tree in Civ5 it was all about allowing you to field more troops and allow those troops to boost other things like culture of happiness.
The #1 none bug problem with the game right now is that the slow tech pace really limits early game options. For instance for the first half of the game every units wears leather armor. You can't limit players this way through tech. Tech should only expand existing options and allow you to do things better, it should not prevent you from doing things at all. Cities and units need to be able to specialize right from the start, you can't require them to research a mid game tech first. Right from the start you should be choosing between light armor, heavy armor, and robes. Early game versions of most buildings and equipment need to be easy to get. The pace of research is just to slow for it to be otherwise.