RPG and adventure games (especially those of Japanese origin, or at least are Japanese inspired) REALLY need to ditch the "collect all the MacGuffins" plots or any variants (destroy/awaken/place the MacGuffin plots) because it turns what would be an otherwise epic story into a scavenger hunt.

The only games I know of that ditch this are the original Phantasy Star games and Chrono Trigger. The first Phantasy Star game in particular does involve hunting down items, but each item on it's own has it's importance instead of just being a number of similar items that needs to be collected, such as weapons that are needed to kill the next boss and all that leads to the final item needed to get to the final dungeon.

Naturally, any JRPG or action-adventure game that does this plot structure would be linear, but if you still want non-linearity, you can just go the WRPG route and have the quests and dungeons be optional tests of skill and experience before defeating the final boss. WRPGs tend to have the whole world open from the onset and the quests and dungeons only exist to leave hints on where to go next. This does handicap the story, but you can make up for it by having backstories and worldbuilding for the characters and setting.

When you see people complain about JRPGs being derivative garbage, this is why. They can all be original if they just drop the "collect the X MacGuffins" plot.