I've encountered glitches, crashes and bugs but I'm not going to focus on those aspects. What really interests me with Fallen Enchantress is the game-play so I haven't kept save-games or kept a stringent journal of bugs. Basically, if the underlying game-play mechanics don't stack up then the bugs don't matter.
There have been a number of aspects discussed about the changes made to Fallen Enchantress and the fact that game-play elements had been removed or changed. These are what I want to focus on initially.
I've played a few games with a couple of races.
Dynasties
Dynasties are gone in FE. Didn't miss them even slightly though. Keep them out.
Without them the game is much more about developing the champions and this really works. It keeps the game focussed on the game and not on a side game. I'm pleasantly surprised no-one has really complained about this in their feedback. This is a mechanic best served with games like Crusader Kings so was a great move removing it from FE. Nice scalpel work there, Derek. 
Cities
A massive improvement but I believe this can be taken even further.
The good aspects are the simplicity and the lack of bloat. Micromanagement is basically gone. Having one production queue works well - either improve your city or build units. You can start to see that city specialisation can work.
The mechanism of having random upgrade traits is a great idea but this can be improved a lot I think. Rare improvements are actually a little too common. I would love to see the improvements linked and enhanced by faction, existing improvements, and technology more than they currently are.
Can see great modding opportunities to improve and extend this as long as the XML is structured well.
The building choice and benefits look simple and functional - which is good.
The garrison system also is great.
Quests
I hated the quests in WoM and I am really liking the changes made in FE. The annoying micromanagement aspects of WoM (escort noblewoman moved 1 square, need to keep returning to huts to get a lame reward etc) are largely gone. You now complete your quest and usually get something quite interesting as a reward.
Some of the mechanics are broken. For example there is a quest where you can win a battle axe but if you refuse to fight in the end, you still get the axe. And in another the description was so long winded that it was confusing what your choice were (overall the text and stories are excellent though and work very well).
Pioneers
The settlement vs outpost mechanic is excellent. It is simple to use and makes a heap of sense. I think I would like a confirmation window when settling though.
I would also like a global toggle to see all food and production values on the map. If there is one I couldn't find it. This would make planning expansion so much better.
So far I haven't been able to test the many cities vs one city balance where a contained city gets a boost. At this stage it seems that if you have grain it is better to always build a city. Wouldn't mind exploring this aspect more in the future.
Champions
Another massive improvement having them recruitable from locations and not wandering about. Also only being able to recruit your 'type' works well - as does the need to research to recruit higher levels.
The choices when champions level up are great but, like cities, this can be improved by making the rare attributes rarer and tying the choices in closer with the champion, faction, and research. Perhaps even tying it in with items.
Before playing the beta I was concerned about champions being too powerful and that the game was going to be focussed around them. Well the champions ARE powerful (or can become so) and the game really is focussed around them - but this works! They are the biggest 'flavour' element and add a lot to the game. I think I would like to see more though in all sorts of directions. For example, having some more negative traits that can develop, like Clumsy, but more global in their scope. Like a very powerful warlord champion that hinders research.
Champion death with the random wound and teleport back to the home city also works very well. Reduces micromanagement, allowing players to play the game with a degree of forgiveness yet rewarding the players who can use the champions effectively.
The World
The world actually isn't as dangerous as I thought it would be. You can build an explorer unit and without too much trouble make your way pretty much anywhere you like. I guess I would like to see more choke-points or monsters controlling a larger area. I don't want them 'wandering' as such but it would be cool if, like cities, lairs slowly expanded over time and any player who reaches the edge of a lair triggers an attack event.
I'm not missing flying or sailing. The mountains and oceans keep the game strategic.
Another improvement is that the monsters aren't constantly destroying resources and caravans which keeps the annoying micromanagement of WoM in check.
The 'world' aspect is better than 'OK' but not great yet.
Lore
Since reading the novels by George R.R.R.R.R. Martin (Game of Thrones etc) I'm much more forgiving of the lore in Elemental. In WoM I was wanting Lord of the Rings - but I'm content now with Westeros.
Monsters
Good to see more than just spiders now. But I still want more!
Hopefully the game mechanism will allow interesting mods to add new monsters and areas. Could see some of Heavenfall's WoM modded races working well as monster lairs in FE.
Definitely heading in the right direction. I'm sure this is where expansion packs and DLC will help as well.
Tactical Battles
Simple yet works. I really like that movement and attack are separated and not tied to an action-point system. Also getting rid of reaction hits is an improvement. And the initiative mechanism is great. Before playing a tactical battle - if it had been described to me - I would have been very sceptical. But I like it.
Like most of the other changes in FE, it simplifies the 'how' but leaves a lot of strategic choice in the 'what', 'where', and 'why'.
The limited zone of control looks good but I haven't played much with this.
There is also a lot of room for improvement in the maps. Needs terrain modifiers etc. The maps you fight on are just a chess board.
I would also like to see any effects (poison, webbed etc) explained in the unit info card if a unit has been effected.
Also not really sure how pierce / blunt / sharp damage is working. Would be good to have some more transparency about this.
Races / Factions
I played a couple of games as Armarians and as Troggs. I purposely picked races at extremes to see any differences and, pleasantly, each rewarded different game styles. With the Armarians I needed to be much more circumspect while researching and establishing my cities. Magic was all about healing and buffing. It felt right and I was rewarded by playing cautiously. On the other hand the Troggs had trouble getting mana and research but made up for it in brute strength. The Trogg cities were all about building fighting units - and these rocked! Aggressive play was rewarded and it was easy to wipe other opponents in the early game. The early aggression was rewarded with new conquered cities and new troop recruitment centres. Magic for the Troggs was all about tactical battle spells such as Wither and Blinding.
I'm liking the races and factions so far.
Research
Another massive improvement over WoM. Three trees works OK but will hinder pre-requesites if required from a different tree. I guess this could be fixed in the UI by having all trees in a single screen - like Sword of the Stars and Distant Worlds. Would prefer to see all races start with leather armour as this makes a very big difference in battles.
I'm comfortable with research now - but I feel it can still be improved a lot and I also think this is where much of the game balance will need to occur.
Magic
I haven't played much with it but I've really liked what I've seen so far. Each spell book feels appropriate and unique. The spells are useful and interesting.
Armies
I like that the army units are much more subtle in their differences now. In WoM each tech and step was way too dramatic. But FE has struck a nice balance here.
I think initial units do need access to some armour though.
User Interface
Big improvements here as well. I'm not really struggling with it or noticing it much - which is good. It helps yet doesn't fight for attention.
Game Phases
The game tends to move through specific phases:
1. Get your city and economy going
2. Explore and grab champions
3. Expand and get resources
4. Tame the world
5. Conquer your opponents.
But the phases present different sort of opportunities so it isn't the old 'rinse and repeat' cycle that stopped replay value in WoM.
Having said that, I would still like to see more diverse opportunities and threats within the game world to push each game in some really wild directions. Gal Civ did this well with the Galactic Council so perhaps these sort of mechanics could work well here too. Some independent lairs that regularly spawn wandering monsters would also be great.
Overall
Fallen Enchantress is a massive, massive improvement over War of magic in every way. It is approachable in its simplicity yet rewards mastery of its strategic aspects. You can really see that if an aspect didn't fit the new vision it was dropped. That must have been difficult and caused a lot of argument internally but well done for sticking to your guns. I really feel this game is verging on being something quite amazing.
Well done to all involved. 
I haven't really been able to add many 'suggestions' so I hope this has been helpful in some way.