I made an account here just because of your rom hack. Thank you for the amazing work and I'm looking forward to future updates! Here are some of the bugs/feedback that I've noted after just having unlocked Marine Resort in Expert mode, version 3.0.3:
Gamebreaking bugs
Mt. Travail will randomly freeze/crash on the setpiece floors (8 and 16). This was reported in a previous version and supposedly fixed, but it's still happening in v3.0.3. This happened to me when using the free camera as well as after using an attacking move (Nasty Plot). From what I can tell, there's no way to prevent this from happening except hope that whatever you do doesn't trigger it.
The first time you go to Shaymin Village, there is an option to skip the cutscene. If you choose to NOT skip it, once the cutscene ends, your partner's sprite disappears/glitches out and it's possible for the game to freeze. You can avoid this crash by choosing to skip the cutscene.
There is an option to skip the story Volbeat/Illumise cutscene. If you choose to skip, you bypass the usual end-of-day scenes and immediately get warped back to Treasure Town and lose several levels (probably reverts back to the stats you had at the last save or something). I actually quit playing a different EoS romhack because of a similar bug where completing ZIN also hard warped you back to Treasure Town, causing you to keep the ZIN softreset stats instead of your original ones. So I went from level 100 to ~30 or something. Stuff like this is not technically gamebreaking, but one of the few things that would make me (and possibly others) ragequit.
Other bugs
Scorching Sands functions as a physical move, even though it should be a special move (affected by Atk/Def stats and modifiers, not affected by SpA/SpD)
Trying to pick up an object on the ground in manual mode sometimes just won't work and it will skip your turn. This happens most often with guests/escorts but can also happen with your teammates and even your leader.
In Spinda Cafe, when you unlock an unexplored area after a drink, it never actually unlocks anything and kicks you out of the drink menu. You can also unlock the same dungeon such as Oblivion Forest multiple times through different events such as Wynaut once and then later through story progression.
Your Pokemon abilities shown in the Summary screen in Treasure Town are the ones they get post-Darkrai, even when you haven't defeated Darkrai. For example, A-Ninetales shows Snow Cloak / Snow Warning in Treasure Town, but change to Snow Cloak / Cute Charm when you enter a dungeon.
Some move descriptions are incorrect. Example: Dragon Rush says single-target melee when it's a line-of-sight move.
Possible bug: Attacks can miss against a No Guard user (wasn't recording, but it happened with Hurricane Articuno in Hail vs enemy Machop in Lost Wilderness with no other effects that I'm aware of, like Neutralizing Gas)
Possible bug: it seems that if you don't have someone that can walk on water, you will softlock on the Froslass setpiece floor (Crystal Crossing B7F), since you have to cross a 1-tile water spot to get to the stairs, and there's no other way to leave the floor besides getting timed out? Unless I'm missing something...
Possible bug: some Pokemon seem to have abnormally high HP regen rates in snow and hail. For example, K-Vulpix and K-Ninetales both regen 5% HP per turn in these weathers (when they normally regen a lot less in Clear), and it feels like some enemy Pokemon have insanely high regen in bad weather as well when they shouldn't.
The Croagunk Shop does not give you the option to trade for Sylveon's tier 3 item when all other tier 3 Eeveelution items appear.
General feedback
After you unlock Mysteriosity, a lot of jobs can't be done on days with high Weirdness levels because you often spawn the max number of enemies on a floor, which prevents rescue and outlaw Pokemon from appearing (a.k.a. "but where's the target Pokemon?") If it's possible, you should cap the enemy spawns to 15 out of 16 on these floors so there's always room to spawn the target Pokemon. I've even had monster houses spawn nothing because of this.
Enemies on heavy darkness floors will use room moves that can't hit you (such as Draco Meteor) because they only have 1 range under these conditions but they always "see" 2 tiles away. Similarly, enemies standing at the edge of rooms can use room moves that won't hit you in a corridor.
Idk if this is possible but it would be nice QoL to have enemies show up (as red dots) on the minimap based on your whole team's vision at all times. Right now, you only see enemies on the minimap when you're focused on the ally that's "giving vision" of that area. Similarly, it would be nice if stuff like Radar and Scanner Orb applied to everyone. As an RTS player (SC2/AOE4), minimap usability is a huge deal for me.
If there have multiple competing weather abilities, is there a way to randomly decide which one activates at the start of each floor? For example, right now if you have both Drought and Snow Warning in your party, Drought will always activate, never Snow Warning. I've tried changing the party order and using different combinations of weather setters, but it seems like one weather ability always takes priority over another.
It would be cool if you could somehow hack stat caps to be based on the Pokemon's actual stat distribution instead of a flat 999/255/... for everyone. It just feels wrong for Blissey and Bastiodon to eventually have the same HP, Attack, etc. with enough stat boosting items.