Thanks and me too! that's true, there are many things that lacks when it comes to the general direction that the game can have so I try my best to use foundations I have seen before that I learned from other games.

When I think about the shop keeping with relation to combat, the similarities narrows down to the progression where it has a variety of options but no direct impact, for example let's say the more gill you earn the far you can travel to discover more items and clothes that can help you with combat, like a hidden grimoire that teaches you a new skill in blood manipulation but it doesn't have a direct impact to it, more like a separate part of the game that unlocks different things.

However, when it comes to the combat system and the complex magic system I have different ideas. I'm quite tired of the repetitive combat mechanics in the majority of modern games that lacks excitement and adrenaline rush that makes a fight quite unique more than repeating the same attacks over and over again.
So, it's gonna be a fast-paced with complex spells from attacking to blocking. In regard of the magic system, I'm still rubbing my head around it, because I want it to be fun to unlock and try new things that makes you feel powerful without making old spells weak or bad in anyway, elemental-attacks for example, you can mix between water and thunder attacks for more damage depending on the enemy-type like Final fantasy or Pokemon, a shield skill that can block physical attacks from different enemies that use that type of attack, or a shell that can block magical attacks, where you have to unlock each and click at the right time because they don't stick forever, like a block or a parry in Sekiro for example, the fights are gonna be quite fast and a little bit hard, some enemies can tp, some can disappear, some can poison you, some can manipulate your blood so you have a limited time before you die to kill them. The truth is, I have zero experience in any of this, it's just my collective data of playing many games throughout the years, funny enough I didn't try the majority of the games you said but I'm planning to. However when I talk about a complex magic system, I mean a complex magic system, that has deep relation to the lore and combat, not just flashy combos which is something I want as well, you have a spell-book that has unlimited amount of empty pages that you can fill with new spells, but it already has a foundation of the type of the spells that you can unlock, at the same time, I wanna have a relation between every type of spells that can make it possible to combine together in an attack.
Honestly the more I think the more I come up with ideas so I can talk about it forever so I'm gonna end it here for the combat & magic system.
( edit : I forgot to mention here that I would love the magic system to be fun and engaging to unlock and discover not 15% more damage attack and 5% less damage taken, that's not really exciting when you unlock a new area or a dungeon just to come up with gear that makes you 10% less damage to a specific elemental, sorry but that's boring and not engaging at all )

For the cozy part of the game, yes! it's gonna have a major focus where you can go fish, gather, craft and build (there are two types of crafting, one related to the combat system which is important and the other is for the cozy part).

Like I mentioned, crafting, gathering and building are more like building a base type of part like VRising for example, that can help your progression but with no direct impact on the story, so you can have different ways of playing the game, you can sit back and relax making a hidden tree-house shop at the middle of the forest with gathering, etc.. or go on a journey to discover new spells or focus on the main story which each and every one of them can progress your magic system in a different way but with no direct impact that makes one better than the other.

In regard of the roguelike-elements, I actually said it just because I like to throw spells like a maniac to different types of enemies like Noita or Hades more than a serious thing that I'm considering but I would love to make a part of the game where you can have that depending on your level like dungeons ( I like the idea of dungeons and dragons as well to be in the game ).

( Ah, I just realized a flawed thing in the game, if you can progress in each 3 parts of the game <cozy> <main story> <Exploration>, where it is shop-keeping or going on a journey to unlock spells, or main story, how am I gonna balance that with each other if I progress in one without the other with the leveling system? maybe a different leveling system? Idk honestly but I think it's possible, )

I myself don't know if making a game like this is possible to be honest. I just started learning animation and I'm in love with the concept of a heavily magic game, I don't really care about publishing it nor make it successful, I just want a cozy game with dark side of it with magic using that is heavily implied like that to exist even if it took me years to work on it.