There were a few developers I noticed weren't at E3 this year.
Sucker Punch.
Developers of Sly and Infamous. Their last game Infamous second son was released in March of 2014, 3 years ago and since then they've been silence. I'm sure a lot of us were expecting to see their new project at E3 but yet they were absent at the Sony conference.
Rumor has it is a new IP that is an open world western this back up by concept art leaking which is how we first found out about Horizon Zero Dawn.
I think its safe to say whatever they are working will be reveal at PSX in December.
From Software
Developers of Armorcore, Souls, Bloodborne, and of course the one and only Metal Wolf Chaos. Their last game was Dark Souls 3 which released in 2016. But they do have but despite Dark Souls 3 being about a year old we do know they are working on 3 projects one of which is an new installment in the Armored Core series and at least 1 of them will befoe the Nintendo Switch.
http://www.ign.com/articles/2016/09/21/from-software-working-on-3-games-one-of-which-is-armored-core
I do think its possible we will see this new Armored Core at TGS and their Switch project in a Nintendo Direct later this year.
Platinum Games
Best known for Bayonetta, Vanquish, Wonderful 101, Madworld, and Nier Automata. Their last game was in March of this year being Nier Automata but they do have multple teams since we do know they have a new IP in the works that they will own the rights to and a Nintendo Switch game but its unknown if this new IP and Switch game are one in the same. it is worth noting that recently despte Scalebound getting cancelled 6 months ago Kamiya did he is working a new project and when we see it we know it will be his.
http://www.ign.com/articles/2017/06/06/scalebound-director-addresses-cancellation-future-plans
http://twinfinite.net/2017/05/platinum-games-is-working-on-an-interesting-nintendo-switch-game/
Now I do think its possible they are working on Bayonetta 3 since with the PC port doing well and Bayonetta inclusion I do think gaming's favorite witch will be given a complete trilogy. (oh god this is gonna spawn a console in this very thread aint it?)
Retro Studios
Best known for Metroid Prime and Donkey Kong Country Returns. Their last game Donkey Kong Country Returns Tropical Freeze released in Feburary 2014 and yet we know very little of what they are working on. We all thought they were working Prime 4 but Nintendo stated its being made by a new team. Now we have no clue what they are working on though but I think this could be the new IP since Reggie did state in an interview with Fox News lots of new are on the way just a few months ago .
https://www.youtube.com/watch?v=HoVOOjxTbcE
Finally it is worth noting that the composer behind the original Deus Ex is working on Retro's new game.
Personally I see this being an E3 2018 reveal since I don't see this being a Nintendo reveal though I could be wrong.