My answer would be contextually particular depending on the type of game structure he'd be implemented in; the way his unique toolset could best be leveraged varies with the kind of game where he'd be playable.
Knuckles in linear 3D stages like we see in the boost games might be best where a small selection of combat inputs are available and enemies are arranged to encourage certain manners of engagement for timely dispatch and good completion times. These things wouldn't be necessary for success, but knowing what enemy is weak to what attack would be a means of speeding up progress. The levels could also be adjusted to provide pathing options that require players to explore using his glide, climb, and dig abilities. This would provide some good variety to enjoy while players build an understanding of level layouts and allowing the more curious among them to discover potentially more efficient methods of clearing the level. Knuckles' move-set should also lend well to stringing actions to one another through intermediary context to allow more capable players valuable and satisfying ways to deal with challenges: something like getting a boosted launch out of wall-burrows that can be strung to a homing attack and then another dig into the wall without grabbing on. This sort of game would do better to avoid an excess of collectables if the design intent of the stages leaned more toward bolstering the avenues to improve times and enjoy that pursuit. A modified ranking system that has multiple "type" parameters for success such as Speed, technique, enemy elimination, etc. would be a possible inclusion, encouraging replaying the game in different ways to get every A rank variation if you're a completionist. This would make for a lot of replay value. If the discussion were about 2D games and the focus was about collectibles, then I'd be inclined to suggest that the levels be shifted from independent segments into a sort of labyrinthine, Metroid style of configuration.
If the 3D game structure were more like an open world, that's where I'd suggest the inclusion of a generous smattering of collectables hidden in various points of interest or slightly unusual locations to encourage thorough exploration and leverage the perception of Knuckles' as a treasure hunter. Tombs, canyons, ruins, and the like could act as more particular avenues for puzzles and more guided progression to the ends of recovering Emerald Shards or the like as key objectives, each with a focus on one of the character's key traits. As an example, the canyon can focus on gliding, tombs on burrowing, and the ruins on fighting. The Emerald hunting we saw in the Adventure games could be open-ended with environmental clues or could occasionally require success within a time limit. Implementing both could work for variety, especially if you only needed to collect as fraction of the total to complete the game. This would allow players to have more agency in the content they want to engage with so that they can avoid the things they don't consider fun.
Just a few thoughts.