As a pre-orderer I've only got access to play Beta2 recently. Over the weekend I've played extensively, finishing a Spell of Making and a Domination victory respectively. I'll try to give a concise overview of suggestions that I think would improve the fun:

GUI

• in-combat there is no indication of how many shards of what flavor I have. The hint text for Burning Hands says it deals 8 + 4 per fire shard. I would like to see actual shard (or power) indication in the in-combat screen, as well as having the hint text show "Burning hands deals 8 + 4 per fire shard (effective 16) damage"
• during war times, the computer player regularly destroys my resources and I get a message "mine in south-west destroyed". This message should also be part of the "turn messages" in the top-right that I can click to take me to relevant resource
• later in the game the number of resources available on the map is substantial - it would be handy to have some form of resource management screen that shows which resources I have and what city they are linked to; as well as all resources that are currently un-built but are in my territory
• I've not been able to find a way to remove an enchantment that I cast on a unit; it would be good to have an enchantment management screen that shows unit, city, global, etc enchantments, their maintenance cost, and the ability to dismiss an enchantment
• faction and sovereign management: the ability to edit (and delete) user-created factions and sovereigns
• in-combat occasionally a unit loses its spells-and-items options (the relevant screen element isn't displayed)

Balance

• consider having some form of start/early game ranged unit (perhaps "slinger") that have limited range
• Crusade has proven a very potent spell that can make normal units the equivalent of a champion (although by the time you can spam Crusade like that, you are essentially "winning more"). Consider gradually decreasing effect: up to level 5 things are automatic, but there's only an 80% chance for a given level 5 unit to get to level 6 with Crusade - likewise it is a 60% chance to get to level 7, 40% to level 8, 20% to level 9, and 10% for every successive level after that
• alternatively: a global enchantment Righteous Crusade with a steep per-turn cost (say 10 mana per turn), could guarantee level progression of all units when using Crusade. In that case consider having Crusade only work up to level 5, unless Righteous Crusade is cast, in which case it has no cap

Gameplay

• more low-level spells should be incidentally all over the world, similar to the random items that the sovereign/champions can pick up. Perhaps 20-25% of the item-locations could be spell locations
• new type of strategic resource, when controlled grants the sovereign access to a particular spell (or even set of spells); but those spells are lost when an enemy destroys the resource structure
• I've seen this mentioned before: outpost specialization. This shouldn't be up-front (a pioneer is still built and set to "Outpost" at a location), but once it exists, an outpost should be click-able and have a once-off selection of implementations ("Fort", "Temple", etc). The relevant options would not be available initially but get accessed as part of research successes. Example of interesting option: "Abyssal Warren" has a 2% chance per season to summon a demon - the demon has a 90% chance to be under the owning faction's control
• likewise, there should be outpost-targeting spells. For example, Arcane Sentry could be an outpost enchantment that increases the sight-radius around the outpost by 2
• I'd like to see many many more unit traits - including very powerful unit traits that count as more than 1 trait for the purposes of unit design
• I've heard mention of random events, but I've not seen any yet. There should be minor to world-changing ones of beneficial to catastrophic nature ("city experiences economic boon for 4 seasons", to "all food yielding squares on the map yield one less food, permanently"). World-changing random events should possibly be part of the game options "yes I do/no I don't want world-changing events"

Factions

• I've heard mention that faction diversity is an active area of development and improvement; regardless I would like to voice my opinion: some (though not the majority of) factions should command a vastly different play experience by having radically different faction benefits/penalties. Some typified examples:
  
  
• angelic pact kingdom: a chance each season to receive random angelic summons. The level of these would depend on the life-magic mastery of the kingdom, and the frequency would depend on the diplomatic capital of the kingdom
  
  
• demon descension: all champions hired are automatically possessed by demons, grants various traits/immunities to the champions; the faction is automatically at war with every other faction - except for vassal factions that pay seasonal tribute; growth reduced
  
  
• empire of pawns: all units have a -5 strength and constitution penalty; units cannot increase beyond level 5, all units are 50% cheaper to build and maintain, faction starts knowing "Company" unit size and cannot build smaller unit sizes; this faction cannot hire champions (though it can receive champions from quests)
  
  
• elemental domination: city growth reduced by half, enslaved elemental spirits supplement city defenses (level and number based on elemental shards controlled); grants elemental summoning spells, grants higher level elementals based on the lowest number of elemental shard (in other words ideally you want an even distribution of fire, earth, water and air shards); this faction cannot use life or death spells at all (not even via champions)
  
  
• nation of heroes: unit composition cannot be increased beyond basic 3-per-unit; unit costs increased 50%; all units have great potential (+50% experience); all units gain +1 dodge, strength, dexterity, constitution and intelligence each level. Units may have up to 5 traits