Just finished (both the "akira" ending and the "disconnect" ending). Great game !
Really enjoyed it.
Came here to see what was the general interpretation of the game as I have mine but it is still unclear...
In a nutshell, more than trying to explain what is going on exactly and if there really is a story (which, doesn't matter that much to me, it's always less important that the message that is being conveyed).... I think that Inside is just telling us to go outside.
Outside, in the open, but also, outside of a system...
I see the progression of the game as a collection of sets that, more or less, are a take on our world : a corrupted nature (pigs "that didn't make it to the market") and then you go deeper into a more technological environment where you encounter mind controlled workers and surveillance devices and you have to blend in with those workers... and then you have those human experiments (trying to produce better "workers" ? Playing "gods" ?).. and the world is literally upside down with water on the ceiling... etc...
It seems the message is : break free from all of this. That in the end, the only thing that we need is simplicity (it ends where it started, in the woods, in nature, with the sun which could be interpreted as a ray of hope, or, simply life)
The second ending is, well, if the first ending didn't convince you to go outside and you wanted to continue playing and did find every secret then : disconnect !
It's just the same message as the first ending but more abrupt...
Anyways, sorry for the rushed/confused impressions/interpretation but it is late here and I'm tired.