No, /etc/rc.local was untouched. The file was empty besides of an "exit
0".

/etc$ sudo fgrep -ril powertop *
/etc$ sudo fgrep -ril autotune *
both give an empty result.

I installed TLP again, which automatially removed package
"laptop-mode-tools".

Using powertop, I've set back the two USB devices to "Bad" again, just to see 
what TLP
does to it.

Before I started TLP, the output of "tlp-stat -u" was:

Bus 002 Device 004 ID 046a:0023 control = auto, autosuspend_delay_ms =
2000 -- Cherry GmbH CyMotion Master Linux Keyboard G230 (usbhid)
Bus 002 Device 003 ID 046d:c24c control = auto, autosuspend_delay_ms =
2000 -- Logitech, Inc. G400s Optical Mouse (usbhid)

Note that 2000 ms of autosuspend_delay is pretty much the time I
experienced for the devices to become unresponsive.

Then I started TLP with a

sudo tlp start

Now that TLP was started, the output of "tlp-stat -u" was:

TLP started in AC mode.
Bus 002 Device 004 ID 046a:0023 control = on,   autosuspend_delay_ms =
2000 -- Cherry GmbH CyMotion Master Linux Keyboard G230 (usbhid)
Bus 002 Device 003 ID 046d:c24c control = on,   autosuspend_delay_ms =
2000 -- Logitech, Inc. G400s Optical Mouse (usbhid)

Basically that means that TLP disables autosuspend in AC mode.
Both devices are working great, like the way they did with the
workaround using powertop after every reboot. With TLP enabled, everything 
still works after a reboot. I also can type in my login password without loss 
of the first characters.

Same for battery mode:
sudo tlp start
TLP started in battery mode.
tlp-stat -u
Bus 002 Device 004 ID 046a:0023 control = on,   autosuspend_delay_ms =  2000 -- 
Cherry GmbH CyMotion Master Linux Keyboard G230 (usbhid)
Bus 002 Device 003 ID 046d:c24c control = on,   autosuspend_delay_ms =  2000 -- 
Logitech, Inc. G400s Optical Mouse (usbhid)

Now that my computer had autosuspend enabled after a reboot (before I 
reinstalled TLP), which
package was responsible for that? laptop-mode-tools?

If laptop-mode-tools enabled autosuspend for input devices, even in AC
mode, that should be avoided with the behaviour I experienced. That
said, I think this issue is not related to the linux kernel at all, but
to one of the power saving tools.

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https://bugs.launchpad.net/bugs/1603659

Title:
  Power Management: USB mouse and keyboard laggy and loosing events

Status in linux package in Ubuntu:
  Confirmed

Bug description:
  This issue is a regression after update to 16.04 (coming from 14.04).
  To my knowledge, I was using TLP together with 14.04, which got
  removed during the upgrade in favour of upower.

  Two devices behave unexpected reproducably after a fresh reboot:

  Bus 002 Device 004: ID 046a:0023 Cherry GmbH CyMotion Master Linux Keyboard 
G230
  Bus 002 Device 003: ID 046d:c24c Logitech, Inc. G400s Optical Mouse

  It looks like a power management related issue. By default,
  - USB mouse pointer is invisible and mouse looses any event unless I press a 
mouse button (which also is executed in a dangerous manner at the last position 
of the invisible pointer)
  - USB keyboard is inactive unless I press a few keys. These first characters 
get lost in the output
  - This happens directly after reboot (e.g. first characters of password get 
lost, mouse is invisible).
  - After login, it still happens: After a few seconds of inactivity, mouse and 
keyboard are non-responsive again.
  - In addition, I also experience lost events without any delay from time to 
time
  - In addition, scrolling with the mouse is laggy in particular

  Most of these problems are gone as soon as I disable powersave in
  powertop for mouse and keyboard:

  Bad Automatische Bereitschaft für USB-Gerät G400s Optical Gaming Mouse 
[Logitech]
  Bad Automatische Bereitschaft für unbekanntes USB-Gerät 2-1.2 [046a:0023]

  The only remaining problem is laggy scrolling and sometimes loosing
  events like keyboard presses, but this could still be another issue.

  The powertop status of other USB devices does not have an effect on
  this workaround. However, the workaround via powertop is lost after
  next reboot.

  It also has no effect when changing USB-Ports or USB-Controllers. I tried
  - built-in USB 2.0 Ports of my DELL Latitude E5510 (1d6b:0002)
  - replicated USB 2.0 ports of my docking station PR02X (1d6b:0002)
  - PCMCIA USB 3.0 Express card (1d6b:0003)

  Accordingly, this issue is not related to particular USB
  controllers/hubs. Plus, as two non-related USB hardware devices are
  concerned, this issue also might not be related to particular USB
  devices, bat rather affect many USB devices.

  I don't experience any problems when using the built-in keyboard of
  the DELL Latitude E5510.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: linux-image-4.4.0-31-generic 4.4.0-31.50
  ProcVersionSignature: Ubuntu 4.4.0-31.50-generic 4.4.13
  Uname: Linux 4.4.0-31-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  thomas     3933 F.... pulseaudio
  CurrentDesktop: GNOME-Flashback:Unity
  Date: Sat Jul 16 17:43:05 2016
  HibernationDevice: RESUME=UUID=28eded29-f9e6-44b5-9e54-c4dd60c8e3cd
  InstallationDate: Installed on 2014-11-29 (595 days ago)
  InstallationMedia: Ubuntu 14.04.1 LTS "Trusty Tahr" - Release amd64 
(20140722.2)
  MachineType: Dell Inc. Latitude E5510
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/@/boot/vmlinuz-4.4.0-31-generic 
root=UUID=6408c2d9-1b60-43d7-9a7f-2dceeb40de28 ro rootflags=subvol=@ quiet 
splash vt.handoff=7
  RelatedPackageVersions:
   linux-restricted-modules-4.4.0-31-generic N/A
   linux-backports-modules-4.4.0-31-generic  N/A
   linux-firmware                            1.157.2
  SourcePackage: linux
  UpgradeStatus: Upgraded to xenial on 2016-06-15 (30 days ago)
  dmi.bios.date: 12/06/2013
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A16
  dmi.board.name: 023HKR
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A00
  dmi.chassis.type: 9
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: 
dmi:bvnDellInc.:bvrA16:bd12/06/2013:svnDellInc.:pnLatitudeE5510:pvr0001:rvnDellInc.:rn023HKR:rvrA00:cvnDellInc.:ct9:cvr:
  dmi.product.name: Latitude E5510
  dmi.product.version: 0001
  dmi.sys.vendor: Dell Inc.

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