I'm running Arch with kernel 4.3.3. I don't have issues with screen flickering with the HDMI output or with the mini-DP output connected to HDMI via an adapter (both times at 2560x1440@60p). I don't have a (working) mini-DP to DP adapter, so I haven't tested native DP. AFAIK connecting a HDMI adapter switches the DP into HDMI signalling mode, so it may not be exactly the same.
I don't have any wifi issues. I did install crda / wireless-regdb and that killed almost all of my 5 GHz channels for some reason (causing the adapter to not see my AP), uninstalling wireless-regdb fixed that. I guess the adapter then uses an internal list and that is somehow more permissive than the correct one.
So I cannot confirm the wifi issues, but I'm using a different distribution and kernel. The mini-DP works at the very least in HDMI mode. What is your resolution / refresh rate?
I'm having almost the same issue with NUC6i5SYH DP flickering but weirdly with certain monitor.
When connecting LG 31MU97-B 4K cinema resolution (4096x2160) display through mDP to DP cable, the monitor starts to flicker and is turning off and on randomly. Doesn't depend on resolution nor Hz I chose, flickering is continuous.
Tried different pc with NVidia GTX970 card and LG monitor was all ok, no issues.
Then tested NUC with another monitor Dell U2412M (1920x1200) and connecting it to DP was working fine, no flickering issues.
I'm using latest bios 0033 and latest graphic drivers 126.96.36.19952.
So, what could be the problem?!
I get this with my new unit and I am using HDMI. My prior system (a Dell notebook) had no flickering, but was using a much older Intel GPU (HD3000 series). This is very annoying, so I'm hoping somebody can help. I have the latest drivers installed, but not the latest BIOS. I'm nervous to update the BIOS right now. It seems many folks have had problems with the BIOS update.
Regarding your problem with the wifi ("The wifi is also disabled when I boot into Xubuntu around 50% of the times I boot up the unit"), does it affect only the 5GHz band, or the 2.4GHz band as well? I am asking because about half the time I lose the 5GHz band when rebooting my NUC6i5SYH.
I am using Windows 10, so if you have the same issue with Xubuntu it has to be a hardware or BIOS issue.