Factorio could be considered as well. It focuses on resource gathering and management, automation, and building up a base. Stone Story also has elements of resource management and building up your character's capabilities or inventory, so there are definite similarities there.
Momodora: Reverie Under the Moonlight. It has a side - scrolling platformer style like Cave Story. The game has a charming art style and challenging gameplay. There are boss battles that require skill and strategy, much like in Cave Story. Also, the environmental design in Momodora gives a sense of immersion similar to what Cave Story offers.
Sushi Story could be considered. It's all about running a sushi restaurant. You create different sushi dishes, decorate your sushi place, and attract customers. The gameplay mechanics of serving customers and growing your business are comparable to Restaurant Story.
I would say 'Dragon's Dogma'. It has real - time combat like 'The Last Story' and also features a large, detailed world to roam around in. You can form a party with different characters, which is a similarity as well.
Final Fantasy XII is also comparable. It has a large and detailed world, and the combat system involves a degree of strategic planning. The gambit system in Final Fantasy XII is somewhat similar to the strategic elements in Vagrant Story where you need to think about your actions in combat. Additionally, both games have a rich lore and interesting characters.
Binding of Isaac: Rebirth has some similarities. It has a lot of items to discover and a procedurally generated world, which gives a sense of exploration like Cave Story. The action - based combat and the need to constantly adapt to new situations are also comparable.
One more game is 'Long Live the Queen'. Here, like in 'Maid Story', you have to manage different aspects. In 'Long Live the Queen', you're managing the life of a princess, making choices about her skills, relationships, etc. It has that element of strategic decision - making which can be related to 'Maid Story'.
Flyff (Fly for Fun). It has a similar style of character progression where you level up and gain new abilities. The flying system in Flyff is really cool and adds an extra dimension to the gameplay, just like Maple Story has its unique features.
Project Runway Mobile. It focuses on fashion design and runway shows, much like Fashion Story which is also about the fashion world. You can create unique outfits and see them on the virtual runway. Another is Style Savvy: Fashion Forward. This game lets you run your own boutique, manage inventory, and style customers, just like in Fashion Story where you manage your fashion - related things. Finally, there's Fashion Famous where you compete with others in fashion battles by creating the best looks.
'Gris' has a beautiful art style and a story - driven gameplay. While it's more on the emotional and artistic side, it shares with Tiny Bang Story the aspect of taking the player on a journey through different environments. You progress through the game by interacting with the world around you, much like in Tiny Bang Story.
For a game like 'Portal 2', the unique gameplay mechanics of using portals are integral to the story. As you progress through the levels using your portal - creating gun, the story unfolds, revealing the mysteries of the Aperture Science facility. The puzzles you solve with the portals are directly related to the narrative, and it's a very engaging way to tell a story through gameplay.