So how about Zelda 1 clones? Open world, over head action RPGs where progress is different based upon which order you tackle dungeons and collect items. Eg "If I beat Dungeon 4 first and get the ladder, it will be harder to pull off, but I'll get some health upgrades earlier".
It's not a modern indie game, so it's slightly out of the intended scope of this thread, but if you never played Neutopia on TG16 (or even heard of it like a lot of people) you should check it out.
It's a pretty good - if also pretty blatant - Zelda 1 clone. It was re-released on both Wii VC and PSN I believe.