Players suffocated to death many many times crossing nether portal from either side. From first person perspective, sometime I died immediately due to suffocation. If I move quickly as soon as the loading screen is over, I may (10%-20% chance, with iron armor) survive. Form 3rd person perspective, the player was suffocating while standing in the portal (His screen was still showing "downloading terrain"). There isn't any block around the portals. Moving the portal and changing the size (to 3x3) does not help. It seems like the portal (purple thing) are solid blocks at receiving side.
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I can replicate this; version 16w04a; Windows 7 x64; java build 1.8.0_73-b02
Not only did I die instantly when returning from the nether, but none of the items in my inventory dropped anywhere. They simply vanished.

I'm still having this problem in 16w06a.
I'm in a multiplayer LAN world and I take damage in portals (about 16 hits), while the host player doesn't.

Im running a MC 1.12.2 Bukkit server and have the same issue. Two times players in my server get suffocated when enter in a Nether Portal, besides that any item in their inventory simply vanishes.