I've got a 15 inch MacBook Pro (mid-2015) - 2.8GHz i7 - basically a brand new machine. Came with El Capitan (now 10.11.1), didn't migrate apps from my last MBP, just installed everything fresh and copied over some folders w/ data. When leaving the machine on overnight (lid open, Mac drops into sleep mode) the Mac will not wake - this happens 1-2 times per week. It will slowly display a login but the KB is unresponsive. Mouse pointer moves but is not clickable.
If I wait around long enough (usually 5-10 minutes) I start seeing notifications about email pop up. I've even tried typing in my PW at the login screen even though it was unresponsive and a few minutes later the astericks appear in the PW area, but it can take another 5 minutes. Even then, the machine is unusable and I have just power the MBP down and restart from scratch - a full reboot.
My MBP is connected to an Elgato Thuderbolt expansion hub with a Magic Trackpad 2, an MS Ergo KB and a Dell 4K display running max res. I run the displays side by side to have as much real estate as possible.
Reading through this thread I upgraded my copy of VM Ware from 6.X to the latest 8.1, though I normally don't have it loaded (and in fact it wasn't running on my most recent lockups) - I doubt this was the cause but upgraded nonetheless.
I run Time Machine and it's backing up to a NAS based array (Synology device on network). The lockups MAY have been happening when TM was trying to perform backups. Looking through the logs via console I'm seeing quite a few messages indicating things were starting to go bad. Some selected events leading up to attempting to wake the machine:
12/12/15 9:51:16.000 AM kernel[0]: Sandbox: tccd(277) deny(1) mach-lookup com.apple.lsd.modifydb
12/12/15 9:51:16.257 AM tccd[277]: LaunchServices: disconnect event received for service com.apple.lsd.modifydb
12/12/15 9:58:27.130 AM WindowServer[165]: send_datagram_available_ping: pid 1124 failed to act on a ping it dequeued before timing out.
12/12/15 9:58:27.000 AM kernel[0]: IOThunderboltSwitch<0>(0x1)::listenerCallback - Thunderbolt HPD packet for route = 0x1 port = 10 unplug = 1
12/12/15 9:58:27.000 AM kernel[0]: AppleThunderboltDPOutAdapter<0>::hpdStateDetermined - deactivate paths
12/12/15 9:58:27.000 AM kernel[0]: IOThunderboltSwitch<0>(0x1)::listenerCallback - Thunderbolt HPD packet for route = 0x1 port = 11 unplug = 0
12/12/15 9:58:27.663 AM WindowServer[165]: handle_will_sleep_auth_and_shield_windows: Deferring.
12/12/15 9:58:27.667 AM WindowServer[165]: CGXDisplayDidWakeNotification [405928712853659]: posting kCGSDisplayDidWake
12/12/15 9:58:28.000 AM kernel[0]: IOThunderboltSwitch<0>(0x1)::listenerCallback - Thunderbolt HPD packet for route = 0x1 port = 11 unplug = 1
12/12/15 9:58:28.000 AM kernel[0]: IOThunderboltSwitch<0>(0x1)::listenerCallback - Thunderbolt HPD packet for route = 0x1 port = 10 unplug = 0
12/12/15 9:58:28.000 AM kernel[0]: AppleThunderboltDPPathManager<0>::createPath - path type 0x1: Initial Credits [int=0 src=0 dst=0] NFC Credits [int=14 src=11 dst=14]
12/12/15 9:58:28.000 AM kernel[0]: AppleThunderboltDPPathManager<0>::createPath - path type 0x2: Initial Credits [int=2 src=4 dst=1] NFC Credits [int=0 src=0 dst=0]
12/12/15 9:58:28.000 AM kernel[0]: AppleThunderboltDPPathManager<0>::createPath - path type 0x4: Initial Credits [int=2 src=7 dst=1] NFC Credits [int=0 src=0 dst=0]
12/12/15 9:58:41.651 AM watchdogd[797]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
12/12/15 9:58:46.853 AM spindump[1074]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-12-12-095846_Browncoat-3.user space_watchdog_timeout.spin
12/12/15 9:58:46.877 AM watchdogd[797]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-12-12-095846_Browncoat-3.use rspace_watchdog_timeout.spin)
12/12/15 9:59:06.708 AM watchdogd[797]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
12/12/15 9:59:09.374 AM spindump[1074]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-12-12-095909_Browncoat-3.user space_watchdog_timeout.spin
12/12/15 9:59:09.377 AM watchdogd[797]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-12-12-095909_Browncoat-3.use rspace_watchdog_timeout.spin)
12/12/15 9:59:15.796 AM WindowServer[165]: send_datagram_available_ping: pid 935 failed to act on a ping it dequeued before timing out.
Having been developing on Macs exclusively for the past 8 years with zero issues like this, it's a bit disconcerting.