I’m back with a few updates. In the end, cpufreq=xen does not seem to have changed anything. The good news, I don’t have the sys-net never loading problem anymore, sys-net always ends up showing after 2 minutes. Possible enhancement is that this time I went with Debian templates instead of usual Fedora. However, a lot of qubes often fail to load at first attempt (including all sys-* qubes), still saying cannot connect qrexec agent for 60 seconds. System is barely usable now in 4.3, but having to reattempt a few times to load my qubes, it is so frustrating that I have to manually restart my all qubes setup several times at each boot to get it working…
Anyway, I’m pretty sure now it is not related to HDD nor SDD in the end (I’ll see if I can edit the title). I love 4.3 and the many enhancements provided, especially in the UX, but the whole system is such a pain to run that I’m definitely considering downgrading to 4.2.4, despite the EOL. Things seem related to Is 4.3 sluggish for you? so I’ll keep updated on this topic, hoping an enhancement for 4.3 may be found soon.