Is there an interesting way to further integrate Subject 4 into the story? We already have the character coming in to solve clues in clutch situations, or to help direct the team on things they should do (ie: contact John Doe). Are there other things that Subject 4 could actually be doing somehow within the story? The big part of the Season 1 finale came from the reveal that the audience had been a contributing character leading up to that point, but it feels like Subject 4 isn't actively contributing as much.
In Season 0 (might have been early S1) when the emulator arrived, it was ascertained what this device was for before there was actually a use for it. When the Apple II was revealed, the dots were immediately connected and I think that made Subject 4 feel like they were actually useful; Without that information it feels like we could have watched the team spinning their wheels for an episode or two before making the connection themselves. Are there more opportunities to feed Subject 4 with clues that they can solve before they're required by the story so that when it comes up you can flashback to Subject 4 already making the discovery?