Honestly "it’s this game but with that." could be a pretty good way to innovate unless you're totally phoning it in IMO.

Metroid was created when people at Nintendo wanted to combine the skill-based platforming of Super Mario Bros with the exploration of a Zelda game. That ended up being one of the two founding games in the Metroidvania genre.

System Shock was created by people who wanted to make a game with the same "emergent gameplay systems as a puzzle/playground" aspect of dungeon crawling RPGs like Ultima, but in a SciFi rather than fantasy setting. What we ended up with was something that combined fast paced shooter gameplay and a tight narrative presentation on the one hand, with letting the player make their own solutions to levels by manipulating open-ended gameplay systems on the other. This is very similar to the situation with metroid IMO, in how it tried to combine two very differnt styles of gameplay. Today we have an entire genre of games inspired by System Shock called immersive sims (though its more of a design ethos than a genre IMO).

The famous level design and exploration of Dark Souls was inspired by the 3D Zelda games, and while I don't have a source for this its hard for me to believe that the lock-on mechanics and basic idea for the movement weren't at least a little inspired by Zelda too. Or, in other words, Dark Souls is basically a 3D Zelda game but with the tone and difficulty of their earlier King's Field series.

Now, I don't mean to imply that combing two good things is a guaranteed way to get something good. Or even that, if you do hit upon a good combination, that that's the only thing you need to put into your work. The games I've just talked about are all absolute classics and obviously a lot went into that. For example, the genesis of the iconic multiplayer aspect of Fromsoft's games came about during the development of Demon's Souls, when Miyazaki was trying to drive up hill in a bad snow storm. There was a line of cars, and when one began to spin it's tires then ones behind it would intentionly push on it to help it up. This all happened without the drivers being able to talk to each other, and, seeing this, Miyazaki wondered what became of the last car in the line, but knew he would never get an answer since he would never see these people again. It was this experience that inspired the creation of phantoms.

However, what I am trying to say is that taking something you like and understanding what makes it tick, then making it work in a new context, can end up creating something that then seems wildly innovative in that context.

As an aside, both Zelda and King's Field were inspired by a dungeon crawling game called "Wizardry: Proving Grounds of the Mad Overlord". Both Wizardry and Ultima were derived from earlier games that were basically "Dungeons and Dragons, but on a computer". Some of them were even named "DND" on the early computer systems they ran on.

DnD itself was created when people wanted to do wargames with a greater emphasis on unconventional warfare (such as spying, diplomacy/intrigue, propaganda, etc) that by necessity required roleplay. After one of these kinds of games was set in a half Conan the Barbarian half Gothic horror medieval fantasy setting with a spooky underground labyrinth beneath a town we got the trope of dungeon delving and returning with treasure to a (relatively) safe town just outside the dungeon entrance.