I love Roguelikes (like Rogue!). The rules of a roguelike are kind of specific (random generation is a big part of it), and Yoshi's Story probably doesn't qualify, but it definitely has kind of a Groundhog Day vibe, like Dead Rising and Breath of Fire V. Except in those games, you power up each time...
Yoshi's Story does have a weird kind of structure, but does it really differ from any dense, linear game that encourages exploration and mastery? Like even Super Mario Bros.? The difference, I guess, is that YS is a bit more (less?) explicit, with the melon thing. The elective difficulty is sort of similar to that of Wario Land: Shake It, though, as well as, apparently, Good Feel's follow-up, Kirby's Epic Yarn. Maybe those guys were big fans of Yoshi's Story? Kirby certainly has a similar aesthetic.
Starting with Donkey Kong, and even leading into Mario Bros. and Super Mario Bros., scoring actually used to be a significant part of Platformers, before they became all about getting to the end and unlocking levels. Nintendo has sort of tried to bring that back a couple of times, with Yoshi's Island, Yoshi's Story, Yoshi's Touch and Go, and Donkey Kong Jungle Beat, as well as Mario Vs. Donkey Kong. Jungle Beat had a particularly fresh scoring system, being a combo-based platformer. I'd really like to have seen how they could've expanded on that concept with a control scheme that was a bit more reliable and predictable. But, alas, we got DKCR.
By the way, someone actually did make a Roguelike platformer: Spelunky.