I had almost the exact issue described in this bug (the only exception being that in my case the internal keyboard was slow no matter what), and it was completely fixed after the macOS 10.12.4 update.
-- 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/1572739 Title: Mac UEFI boot 24x slower keyboard/touchpad troubled Status in linux package in Ubuntu: Confirmed Bug description: When rebooting after a Linux session, the UEFI and grub boots are extremely slow and the process takes 3 minutes - As soon as the kernel boots, ie. luks input, everything is fine again - OS X boot and option-boot is slow too, fast after FileVault password input - Internal keyboard and touchpad is extremely slow, like 30 s per key press. - Plug in usb keyboard and mouse: works fine, while the internals are still slow After an OS X ession upgrading to 10.11.04, the boot got fast again - After the net Linux session, back to slow Impact: boot takes 3 minutes get-around: lots of patience, possibly use of external usb keyboard first discovered on 15.10, exists on 16.04 ProblemType: Bug DistroRelease: Ubuntu 16.04 Package: linux-image-4.4.0-21-generic 4.4.0-21.37 ProcVersionSignature: Ubuntu 4.4.0-21.37-generic 4.4.6 Uname: Linux 4.4.0-21-generic x86_64 ApportVersion: 2.20.1-0ubuntu2 Architecture: amd64 Date: Wed Apr 20 14:29:51 2016 HibernationDevice: RESUME=/dev/mapper/C89-SWAP MachineType: Apple Inc. MacBookPro12,1 ProcEnviron: SHELL=/bin/bash TERM=xterm-256color PATH=(custom, user) LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8 ProcFB: 0 inteldrmfb ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.4.0-21-generic.efi.signed root=/dev/mapper/C89-RFS ro quiet splash vt.handoff=7 PulseList: Error: command ['pacmd', 'list'] failed with exit code 1: No PulseAudio daemon running, or not running as session daemon. RelatedPackageVersions: linux-restricted-modules-4.4.0-21-generic N/A linux-backports-modules-4.4.0-21-generic N/A linux-firmware 1.157 SourcePackage: linux UpgradeStatus: Upgraded to xenial on 2016-04-19 (1 days ago) dmi.bios.date: 10/26/2015 dmi.bios.vendor: Apple Inc. dmi.bios.version: MBP121.88Z.0167.B15.1510261437 dmi.board.name: Mac-E43C1C25D4880AD6 dmi.board.vendor: Apple Inc. dmi.board.version: MacBookPro12,1 dmi.chassis.type: 9 dmi.chassis.vendor: Apple Inc. dmi.chassis.version: Mac-E43C1C25D4880AD6 dmi.modalias: dmi:bvnAppleInc.:bvrMBP121.88Z.0167.B15.1510261437:bd10/26/2015:svnAppleInc.:pnMacBookPro12,1:pvr1.0:rvnAppleInc.:rnMac-E43C1C25D4880AD6:rvrMacBookPro12,1:cvnAppleInc.:ct9:cvrMac-E43C1C25D4880AD6: dmi.product.name: MacBookPro12,1 dmi.product.version: 1.0 dmi.sys.vendor: Apple Inc. To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1572739/+subscriptions -- Mailing list: https://launchpad.net/~kernel-packages Post to : kernel-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~kernel-packages More help : https://help.launchpad.net/ListHelp