There were a few reasons for that... One, we had to make some tough design choices, take the Misty Woods as an example: The idea was that we give the player the feeling that he's lost in a forest that constantly changes around him. Now, after we designed the area, we knew there'd really be no proper way for the player to go back in and re-traverse the entire area, so we could have either not put any 'valuable' items in the area or assume that people are okay with playing through the game again.
Two, there are story-events happening in the game that sort of prevented us from having the player go back to a certain location... The Ginso Tree is flooded with water after Act1, so we dabbled with the idea of having the player being able to re-enter the now flooded Ginso Tree, but it also wasn't really designed for underwater gameplay and I always wanted to ensure that if a player has to re-traverse, the area should still contain enough interesting, new things for the player to discover... And we just didn't have the time to iterate over everything again after we wrapped the main designs.
Since a hell of a lot of people are still playing games like Super Metroid to this day, I thought it was an okay decision to make. I understand that a lot of people want to get absolutely everything on their first run, but Ori is designed in a similar way to Super Metroid, A Link to the Past, etc.: On your first run-through, it takes the average player 10-15 hours to complete the game. But when you're on your second run, you can probably cut that time down in half or even more, since you know exactly where to go. So really, I just didn't think it's that big of a deal if people have to play through it again, especially since it's super fun to play Ori
Having said that, we got a LOT of requests from players who want to be able to get absolutely 100% on their first run, so we might look into how we can accommodate you guys with future updates