They don't have to be super rewarding. They just need to be more varied. Take Majora's Mask. Some masks are simply decorative, but some fundamentally change the way you play the game. And you were collecting them because it eventually unlocks the final mask which lets you be the ultimate badass. There's not really an equal reward in BotW. The only one I can think of is Revali's Gale. The Sheikah Slate upgrades aren't life changing. The ability to time stop enemies feels more like cheat mode than something actually cool.
Personally, I don't play BotW for the rewards themselves.
The reward for me in BotW is discovery. I play it for the fun of finding hard-to get shrines and new variations of the Korok seeds puzzles. I'm currently "collecting" 45 Korok seed for a new Meele slot, and that's fun since I can grab the Korok seeds whenever I discover them.
I also have more than 30000 rupees that I want to find things to spend them on. I will still do the side quests, because they generally let me discover new things or new fun NPCs. Not for the rupee rewards.
Upgrading armor is a step in the right direction but most set bonuses are just slightly stronger versions of existing properties. It'd have been more fun if some set bonuses would give you, say, offensive properties like electrocuting anyone who touches you, or unlimited stamina, or the ability to use a two-handed weapon with one hand. What they did now is that you need to change armor because it's too hot or too cold or that the women town won't allow you to enter. They're a barrier and it's obnoxious rather than fun.