I've been thinking about how to approach this and I've come up with the following conclusion:
This game doesn't have to be all that balanced.
This game embraces its random elements and part of the point is that all runs will be different. This means that some will be easier than others. I came here from a roguelikes background and that's part of the fun.
The important thing is that >95% of runs feel beatable if you'd improved your strategy and >95% of runs feel like they required strategic input to complete. Following the main progression of the game, I think this requirement is met for the most part.
I never felt that a dungeon/challenge/puzzle was too hard. Occasionally you'll have a run that seems doomed to failure but it almost always feels like you'd have had a chance if you'd played it better and the times this doesn't happen are very rare. I occasionally felt like an element was too easy but there were always harder things to try instead so this wasn't a problem either.
The problem cases are any items/classes/gods/dungeons/mechanics that remove meaningful strategic choices from the game. I'll list a few (in no particular order) that I can think of.
As a completionist I'm going to want to get all the badges/classes on all the normal dungeons at some point. I went back to one the other day and (even with the vicious token) it was kind of dull. Maybe vicious token should spawn an extra boss in the normal dungeons with only one. That way you can use the token while going for the badges and still have a challenge or you can just not use it if you want an easy run.
It's fine to have some classes stronger than others and they all have a unique play-style requiring different strategies which is nice. The fighter is pretty boring but feels like the introductory class so that's fine.
I think the berserker/monk are a little dangerous design-wise but it feels like the curses and monster damage diversity in the later dungeons is designed to combat this and they end up still being interesting.
beserker/monk/rogue/warlord and assassin are my usual go-to champions when trying a new dungeon as they all have an ability that effectively says you will get (at least) one extra attack in combat. The monster diversity (diff. damage types, first strike, mana burn etc.) makes this OK though as each ability brings different required strategies to utilise effectively.
I mentioned the one I consider the biggest offender in reducing strategic decisions in my other thread and don't want to repeat that discussion here.
Some items are kind of dull in what they bring to the table (think dragon shield) but some of them have to be so that's fine.
Patches: I took patches on a run once and didn't find it enjoyable. I don't plan on ever using it again. I would imagine there are lots of other people who have done the same. I think it needs to be changed to do something more interesting or also provide some tangible benefit (eg. +3gold on level up) otherwise there's no point it being there.
God preps: I've yet to use one as for some reason it doesn't feel right to do so. I've no idea why I feel like this but I'd be interested if others feel the same. If they do then maybe something needs to be done here.
Again the diversity sorts out the balance for itself.
It feels like killing undead was meant to have more of a bonus (uniqueness) associated with it for zombies to be as annoying as they are. I think it's fine to have a monster type that just acts as a roadblock but maybe there should be some minor reward for killing them (eg. +1 exp) just so that they feel more unique.
The other monster type that feels a little boring is dragons and I'd consider a minor change to make them feel more unique too. I can't think of a good one though.
I guess this is the real area where balance actually makes a big difference to the game so I'll go through them in order.
The ENDISWALL boon seems expensive to me. It makes a huge difference whether you find one in the dungeon or not if you're going this route. Maybe it should be split into two (though then binlor has a lot of boons).
10 piety - create an ENDISWALL glyph in the dungeon (only if one doesn't currently exist)
15 piety - teleport an ENDISWALL glyph from the current dungeon level next to the altar.
The few times I've been with binlor I've found it interesting choosing between the boons to maximise resistance pre piety or get other useful effects so the rest seems OK.
I would consider changing the major punishment to - sets resistances to -5% (or -10%) as then it's never free to desecrate the altar as sometimes can happen.
Seemed fine with my little experience.
Has interesting strategic choices. It seems like piety gain on Plantation does not need to be so high. It seems too easy to get to 100 piety.
A lot of interesting choices with this god. I think it's the -10 on a potion that really makes this god interesting.
Oddly I find the 'random' god the most boring. This one seems most in need of a change. It's a huge difference how close to the start of a run you find the altar. The play doesn't feel interesting and the final boon is only so good to balance out the failures of the rest of the god. I don't think a minor change can fix this and the whole thing needs reworking.
This one also seems good/interesting. I get the overall impression that she doesn't punish me all that much and it's mainly easy going. I'd suggest a small punishment on converting glyphs but that's terribly out of flavour with the refreshment boon.
I'd like to see some additional action punished though.
There are enough options here that this is interesting. They all seem to have their uses. I'd like to know what overheal actually means (hopefully this will be in the codex). I don't understand why you can concensus and then another pact but not the other way round (iirc). It seems to me that concensus should act like all the other pacts.
A little dull. The only really interesting part is assessing whether or not you should take him as a god in the first place. There's not much that can be done without a big overhaul and it's not a big issue.
Another interesting one. I don't have that much experience so can't comment on the finer details but definitely adds to the strategy in the game and doesn't feel too over/underpowered.
We're done!! Thanks for reading.