I want to start by saying, I am EXCITED for this game! So far it's been a fantastic experience. Well, I've experienced all it has to offer up to this point, and I'm ready to poke holes in it.
We'll start with the criticism.
1) My first (major) issue is sustainability in this game. There is too much. Great adventure games get you geared up at home and ready to take on one hell of a dungeon/unexplored region. As it stands now, I never go back to my town unless I have to find more lieutenants/overlords/commodity towers. There's no reason to. I have everything I ever need on the field. Low on health potions? Raid a few houses. Running out of mana? Raid a few houses. Need more wooden platforms (if for some reason you don't have storm dash or ride the lightning)? Raid a few houses.
Possible solutions: Well, the easiest one is pretty simple. Cap your healing potions, and remove them from houses. Instead, make them craftable from a settlement. This gives a reason to come home, and prevents you from forever sustaining yourself out in the wilderness. Only the very skilled can stay out for TOO long. This also makes big boss battles more interesting. However, I don't suggest doing this for mana. Limit the amount of mana potions, but don't remove them for houses. You don't want to punish a player who's extremely good at avoiding damage by forcing them them run out of ammo. But don't make regenerating mana, either! That's taking away from the adventure feel! Running out of mana should only punish a player who's careless with it. This would also be a move towards optimizing the "right spell for the right situation" that you are shooting for.
2) Getting new spells is exciting. If I find me a Sapphire, I want to it to feel AWESOME. I want it to do amazing, and incredible things. It does! For a while. Upgrading spells is boring, and feels like a necessary chore. My awesome spell is just not as good anymore, and furthermore, I have to go do the exact same thing I did before to make it better. And by better, I mean just improving the numbers to be appropriate to my level. It doesn't change in any way, it doesn't do anything new. Just higher numbers. As it is now, you technically aren't upgrading, you're going out and finding a whole new spell. The easiest way I can think of comparing this is with Zelda: Link to the Past. You occasionally get new shields in the game. Every time you get a new shield, it blocks something new, something better. If we implemented AVWW system into LttP, it would work more like "After a while your shield stops working, so you have to do a dungeon to make it work again. The worst part though isn't that it's just a shield. It's the shield, boomerang, sword, etc. etc. and early on by the time you've replaced it all you're almost ready to replace it again. Going out of your way for bread and butter seems off.
Possible Solutions: As far as getting new spells, make it MUCH harder. I mean like, one gem per 5 or 6 levels of caves. And put a boss in there too, or a boss guarding the room to it, always. Maybe even less frequent. Preferrably even less frequent Right now it feels just... easy. But it has to be somewhat easy, because of the current system to upgrade your spells! So instead of getting new gems to upgrade your spells, put those consciousness shards to use for more than just TBS, and use them to upgrade spells you've already gained. Or create a new resource system. Whatever it is, make it fast and easy to upgrade, with components collected along the way of your usual exploration.
3) The Surface. The surface in most areas has some unique mobs and features. And overall it provides virtually nothing but buildings and end points for you. It needs more content! Enough said about that, it's in beta. The only other main issue I have is the negative space on the surface. Some regions nicely solve this (The ones with the eagles and the floating islands all the way to the top are my favorite surface areas x 1000) but most do not. Now, I know there has to be some sort of negative space to the top of the sky to give you the sense that you are outside, but THAT much? Right now I don't think "Wow, look at how vast this feels!" I think, "well, time to pull out the wooden platforms (which is the only reason I ever use wooden platforms) and deal with the amoeba miniboss that rushed to the very top of the area."
Possible solutions: Reduce the negative space between the ground and the top boundary. This also gives more room for bigger and more elaborate surface tunnels.
The rest I will bundle into the group of "I understand it's beta but I thought I'd point it out" Bosses, Items, Events, Enemies, SUITS OF ARMOR, Models, Story, Cave types, Spells, Surface events, Decorations. Need more.
Hmm, I had more when I was typing this out, they kind of floated out of my mind, I'll remember them again.
Suggestions:
Houses: I'd love to be able to build a personal home in a settlement and decorate it. It'd give me some cooldown time in between trips. And it'd give you all sorts of reasons (all one of them) to collect cool things you find out while adventuring.
Pets/Companions: For those who aren't inclined towards multiplayer (I am definitely not one of them, when your multiplayer comes out I'm buying 10 copies), having a pet or bringing one of your settlers along to help could be pretty useful. Might be too much effort for what they offer.
A city of people who do more than complain: I know it's in there. I see it in the folders! But my people are ALWAYS complaining about overlords no matter what, no matter how many I kill. Even my farthest cities complain.
Jet packs: You seriously have no idea how much jet packs improve a games quality. Every game should have one.