The first part is definitely a Compiz problem. 
This strange “ghost window” happened to me for the first time today. Not too long after, Compiz crashed back to Marco… no surprise!
There’s probably a plug-in responsible for that. I had my ups and downs in 15.10 with Compiz before tweaking it to something stable.
I admittedly had a bit of a mixed first impressions with 16.04 – under the hood this thing felt snappier then 15.10, but my problems were because of upstream package changes (lsb is gone - I can’t install my printer driver! 
) and it’s taken me longer to get my installation to my desires.
I agree with the Boutique and that dialog being impractical, I have a plan to change that for 16.10. I did at one point have 20 Apt windows just stacked and let the Boutique do its thing, only telegram failed. I think the apt daemon dying was an isolated case in this instance.
That crash of ubuntu-mate-welcome at the end looked like it was caused by apt once again.
Thanks for sharing your honest thoughts.
Hi @zetakain,
sorry to hear you are having doubts about UM 16.04, simply running a full system update can solve many problems; to which I am sure you are well aware: