I've tried now:
With Ubuntu 16.04.1 LTS:
- Plain vanilla kernels 4.1.x, 4.4.x, 4.7.10, 4.8.x
- Ubuntu-Kernels: 4.5-rc1, 4.5-final, 4.6-final
- fedora mainline kernels (only took kernel-config, compiled kernel myself)
  Result: keyboard, mouse working as expected with all kernels, except
          4.8.6 -- maybe there was a missing configuration option with
                   this kernel. I did not dig into it.

With Ubuntu 16.10:
- Plain vanilla kernels 4.1.x, 4.4.x, 4.7.10, 4.8.x
- Ubuntu-Kernels: 4.5-rc1, 4.5-final, 4.6-final
- Fedora mainline kernels (compiled using Ubuntu 16.04.1 LTS)
  Result: no keyboard, no mouse for all kernels. But to be exact:
  Boot. Wait for Login prompt. For a short time the cursor is
  blinking behind "login:". While the cursor is blinking there, you
  can type! If you are fast, you may even press return, and
  "Password:" pops up. If you have a short password you may now
  be able to type this password and log in. In most cases at some
  point the cursor just vanishes and no further keypress is accepted,
  including CTRL-ALT-DEL. You are locked out.

  This is for all kernels I tested. It does not depend on some special
kernel.

With the help of SystemRescueCD I've booted up and analyzed the logs written by 
systemd: Systemd starts consoles. Then, after starting some further parts of 
the system, terminates consoles. I could not find any console starts 
afterwards. I'd expect systemd to restart any terminated console for as long as 
systemd runs. This does not happen. Systemd is configured to restart consoles, 
but it does not do it. I was not able to find out why.
Networking is started but it seems not to establish network connections until 
users log in. In tune sshd never starts, because network isn't started at all. 
If you manage to login typing really fast, while the cursor blinks behind 
"login:" networking will start! You may be locked out at consoles, because no 
keypresses are accepted any more, but in case you managed to login, 
NetworkManager starts networking for the logged in user and in tune sshd is 
started and you may then login remote.

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You received this bug notification because you are a member of Kernel
Packages, which is subscribed to linux in Ubuntu.
https://bugs.launchpad.net/bugs/1630245

Title:
  after starting ubuntu 16.10 -- no keyboard, no mouse

Status in linux package in Ubuntu:
  Confirmed
Status in linux source package in Yakkety:
  Confirmed

Bug description:
  After starting Ubuntu 16.10 keyboard and mouse are dead. Since it
  works with an older kernel but not with the latest one, I'd assume the
  newer kernel does not initialize the devices the right way.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: systemd 231-9git1
  ProcVersionSignature: Ubuntu 4.4.0-9136.55-generic 4.4.16
  Uname: Linux 4.4.0-9136-generic x86_64
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  Date: Tue Oct  4 15:27:52 2016
  InstallationDate: Installed on 2012-12-12 (1391 days ago)
  InstallationMedia: Ubuntu-Server 12.04.1 LTS "Precise Pangolin" - Release 
amd64 (20120817.3)
  Lsusb:
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
   Bus 002 Device 003: ID 0e0f:0002 VMware, Inc. Virtual USB Hub
   Bus 002 Device 002: ID 0e0f:0003 VMware, Inc. Virtual Mouse
   Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
  MachineType: VMware, Inc. VMware Virtual Platform
  ProcEnviron:
   TERM=screen
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=de_DE.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.4.0-9136-generic 
root=/dev/mapper/test--tps--ubuntu--muc-root ro vga=789 consoleblank=0
  SourcePackage: systemd
  UpgradeStatus: Upgraded to yakkety on 2013-02-11 (1330 days ago)
  dmi.bios.date: 07/02/2015
  dmi.bios.vendor: Phoenix Technologies LTD
  dmi.bios.version: 6.00
  dmi.board.name: 440BX Desktop Reference Platform
  dmi.board.vendor: Intel Corporation
  dmi.board.version: None
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 1
  dmi.chassis.vendor: No Enclosure
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnPhoenixTechnologiesLTD:bvr6.00:bd07/02/2015:svnVMware,Inc.:pnVMwareVirtualPlatform:pvrNone:rvnIntelCorporation:rn440BXDesktopReferencePlatform:rvrNone:cvnNoEnclosure:ct1:cvrN/A:
  dmi.product.name: VMware Virtual Platform
  dmi.product.version: None
  dmi.sys.vendor: VMware, Inc.

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