If you want to avoid farming you could give points for tiles uncovered
imo this is almost as bad as farming for items. It rewards slowly exploring every tile on every floor even when there's no danger or any practical reason to be so thorough.
A good scoring system should be about displaying skill in excess of what survival play demands. Good ways to do this are risk/reward systems like Brogue's lumenstones. Let the player opt in to something dangerous and reward them with a nice score if they pull it off. Optional dungeon levels, Nethack-style conducts, actions that deliberately weaken the player or strengthen their enemies. Those kinds of things make good scoring systems. Shmups are the genre with the most diverse and best-developed scoring systems, so they're a great place to look for inspiration.
You could also just base score on how quickly people complete the game or how far they got if they died. That always works.
Watching the video it looks like the levels are pretty packed with lots of areas to explore, some of which would be hard to spot because of the way the rooms are constructed. If you've also got secret doors, tiles uncovered would seem like a good indication of how well you explored the game. You could give points for each tile depending on depth, such as one point per tile on level 1 and 1.5 points for level 2, 2 points for level 3 etc... If you didn't complete the game that would give you a pretty good indication of how well you've done. You could also give points for monster kills or item pickups, but less than tiles explored, such as 0.1 point per XP cost of monster or 0.1 per GP cost of item.
It's up to you what kind of behavior you want to reward, exploration, looting, combat? Tactics? You could multiply points gained by the difference between player XP and monster XP.
Just ideas.
EDIT:
Forgot to say how great the game looks already
I watched the video and had a look through the blog and I'll be watching eagerly as it develops.
