The damage tooltips are not accurate, they still need fixing.
You can have the potions (any of them) by researching into Magic Tree. The prices are fair, you shouldn't lack money by the time you get with research at that point. The rarity of those curing potions on map is intended because if they were abundant the scars (negative effects if a hero dies in combat) would lose any meaning as you would carry 300 potions to instantly cure the effect.
The summons are fine as they are, if you want to summon powerful creatures use the later summons and don't rely on shadow wolf At level 20 with half of summon tree unlocked, my Sovereign can cast a level 8 shadow wolf who's purpose is to absorb 1-2 hits and possibly deal damage, or a level 20 Air elemental with 160 hp, 60 attk, powerful lightning dmg and impale.
You have several invulnerability (both to physical dmg and magic) in the defender tree. Being active abilities adds choice and awareness to player instead of relying on out of jail card no matter where I move on tactical map and what enemies I face. Good design decision.
Formulas for damage do take defense into account. As stated at start of my post, tooltips are not always accurate, and this will be fixed most likely before release.
Guard works fine as it is, it's purpose is not to make the troops you're guarding invincible (sort of) for a whole turn (like having a cloth wearing mage staying toe to toe with a troll), but to give them a hp buffer until their turn comes, when they can take action and move away from harms way or w/e you see fit for them to do
Heroes at low levels start weak. Yes they can die. Yes you need to be careful what enemies you engage before you get some levels and better equipment for your troops. If you had a demigod from level 1 who could empty handed clear the whole area near your settlement the game would be completely unbalanced and terribly boring.
The price for items at shop, and rushing productions is in a good spot. Gives you an incentive to not IGNORE your economical development and treaties with other players. If you could mass purchase amulets rings new weapons mounts etc as soon as they were available they would lose their flavor and you'd be in a no different situation than generating a lvl 40 hero with best epic gear pretty much
You are not paying attention to your cities development if you can't make it past level 2. In all my games I get several to level 3 and few to level 5. You need to monitor how much growth & food you have available, you should have enough towns in good locations to provide extra food for your conclaves and fortresses, as well as money to support your troops etc. There are magic buffs and special buildings that help with this.
The heroes (as of 0.87) are placed on battlefield depending on their specialization and equipped weapons. My archers and casters (Even if I use a melee weapon on my spellcaster) are always placed behind melee troops. My warriors, commanders, melee Assassin, Defenders are always in the front line. Mind you, if you only have troops with ranged attacks, your hero might end up on same row or in front of them. TIP: mix units, always have melee units to act as a meatshield for your fragile backrow.