I have 2017 XT and will address a few of your points with which I'm personally familiar.
Engine: really vibey. This is my first vtwin and I am coming from a 2017 DRZ400E with knobby tires so was pretty surprised how vibey the engine in mine is.
First, I have not experienced the vibration issues to which you refer. I would suggest, however, checking all fasteners. I'm not a dealer basher; but, I've noticed over the years that all dealers don't necessarily take extreme care in assembly of new bikes. On another note, I don't usually do mods to bikes until after I've had time to get a feel for them. However, with my 650XT I ordered a fork brace from AdventureTech almost immediately. Maybe that's why I didn't experience the vibration issue. The same applies to handling addressed below.
Handling/Suspension: This is the first bike over 200 kgs I have owned so I'm not sure how widespread this issue is but through tight twisties I feel I really have to push on the inside bar firmly and pull the outer bar to get this baby to turn in to get the lean angle I want.
I speculate the handling "difficulty" you explained is mostly due to going from a significantly different handling bike. I'm not saying you are wrong as this is very subjective. I think it will be second nature as you become accustomed to it.
Brakes: At first terrible. Now they have bed in they are OK. I would prefer more stopping power and will most probably upgrade them.
Brakes are kind of similar to the handling difficulty I addressed above. I know they are not as good as the FJR from which I most recently came. I've become accustomed to them and find them quite effective. I actually thought I would upgrade mine; but, after daily use, I have adjusted myself accordingly and find them effective.
Ergonomics: I'm 6ft 33" inseam. My knees were starting to get a bit cramped towards the end of my 4 hour ride today so ideally I'm going to look at getting some adjustable rearsets a bit lower and more forward would sort it.
Ergonomics for you and me are the same. I got Rox up and back 1.25" risers and peg lowering kits from AdventureTech and it's a whole new (and better) ballgame for me.
Wind Blast: I have the factory screen in the highest position and I am getting buffeting from the wind in the forehead area of my helmet from around 90 kmph plus. I can feel the blast from the mirrors too so I'm going to get the mirror risers and a better screen.
Wind blast was cured for me by the Madstad larger windscreen and brackets. These too were a game changer for me.