I also think that the monk got way overnerfed. When I played anything Dungeons and Dragons (DnD) related, I always picked the monk as I really like the theme of anticasters and mind over body.
Then I came to Desktop Dungeons (DD) and tried the monk that had both 50% resistance. It used some time to get used to him and I was a little bit let down that the concept behind the monk here is completely different, especially after the nerf:
Monks in DnD are anti-spellcasters with average melee damage but the ability to punch enemies a lot and an array of special effects to withstand enemy magic and special immunities, without relying on heavy equipment.
On the other side, the DD counterpart is pretty much the opposite now:
Monks are pure endurance fighters without any immunities or special effects regarding combat and in fact magic is their greatest weakness and they abuse inventory like mad.
Thematically, I really dislike the monks here (although I can see and accept the concept they are based on, its just diametric to my own concept).
I'm also tending to the purist side of the game and this is where you can't really compensate the downside of the nerfed monk that much, making the nerf even worse.
I really really like the comment from fall_ark regarding the inventory ability.
What I'd do is the following change:
Make the monks class abilities scale with empty inventory slots.
1 free slot means 10% resistances for both magic and physical damage as well as an increase of 20% regen per tile. The attack bonus is fixed at -25% (you can easily change that to balance the class, regarding vicious I think -50% is too much with this setup) initially and is indepentend of inventory space. The resistance cap, however, is again the normal cap every character uses. Starts with an additional compression seal so that you can use one item.
This way, the monk is naked slightly stronger as he has less attack loss, but the more items you want to use, the harder it gets. You can counter this by using boons that increasy resistance, but all they effectively do is free your inventory for another item instead of giving you the resistance, as this is almost maxed anyway. If you're keen about using magic and/or a special item, you can use the compression scroll (as well as another one you can prep) or you have to be clever about which items you take into your inventory and swap them accordingly. Maybe it is too weak this way but certainly more interesting and less of a nobrainer (at least when the dungeon has curse enemies, because that makes things much more complicated). Also, more in theme with the theme in my head^^