Specifically, I'm talking about stories where the main character figures out creative ways of using the system/magic by experimenting on it and in general just by (eventually) understanding it better than everyone else.

Even more specifically, I will list some stories which are as I described (at least to me) and what about them I liked.

A Budding Scientist in a Fantasy World - I really like how the MC approaches experimenting on the system and slowly learns more about it and magic. She uses her unique insight from being able to see a special kind of 'system' mana to understand how the system works. As of the latest chapters, she is trying to learn how to replicate it. I like how the system is a tangible thing that can be theoretically replicated and not above the laws of the universe.

The Magineer - I like how the MC in this one uses his AI in order to discover the fundementals of magic. This lets him make spells far more powerful than anyone else, for example unrestricted flying, because he has access to more fundemental building blocks for spells. As an example, he makes the first ever spell using conditional logic.

Magic is Programming - Name is self explanatory for this one really. I'm really liking this one and the slow power buildup. One of the things I like about this one is that the MC uses his programming knowledge along with a particularly good translaion spell to understand the exact structure of spells in the way the natives of the world can't (the spells are chanted in a dead language). He uses this knowledge to do some freaky things, like putting in wrong inputs into a spell in a way that someone from the world wouldn't ever try (putting a negative value in for a force, which to him obviously means a force in the opposite direction. And in this world for the spell to stick you need to have the understanding, so anyone else even if they tried it - without that concept in their head it just wouldn't work) and making an infinite mana glitch. Another thing I really like is how he uses his knowledge of computer arcitecutre to make "soul structures" which are essentially a programmable computer. For everyone else in this world, these structures (which essentially give you 10 powers) are immutable and one time. Becuase he made his programmable in a way, his soul structures can do so much more than anyone thought possible. And finally, (spoilers for latest patreon only chapter) He discovers the magic's system version of a help screen/documentation. Since the people of the world think it is natural, and one needs to have a very specific concept in their mind to access something, he is the first to discover this.

I like it especially when the MC learn/discover things nobody has done before/think is impossible. Less so when they're just rediscovering things everyone already knows (unless its early days).

Some things that I like less: I prefer when the MC comes from another world in some sense, because it makes them suddenly discovering things nobody else has even thought of a lot more reasonable. I don't mind either way in the end, just a preference. I dislike harems. I don't mind the uplift genre, however I prefer when stories focus on the character discovering new things from their new environment (in the system/magic/etc) rather than simply copying what they already know directly into the new world. I don't mind when the character uses knowledge and technology from their original world in order to aid in researching or to unlock new abilities, etc through.