WOW! What a list.
The problem with these situations is
1. Deciding what is normal and what is a problem
2. What is acceptable to one person may not be to another
I have done 5,000 miles (8,000kmh) in the past 8 weeks and hopefully have got to know most of my up!s 'characterful' noises.
The engine does rattle at idle, but not excessively and it soon quietens down on the move until you reach 4,000 rpm, when the 3 cylinder rumble sets in - a not unpleasant noise I might add.
The thing I still find at-odds with the rest of the car is the gearbox noise - whether mine is better or worse than average, I don't know, but what I initially put down to engine noise is, I am now pretty sure, the gearbox. The 'clattery' nature of the gearbox in 1-4th gear appears to be down to gear cluster rattle and gets worse as the car gets fully warm - and the gearbox oil warms through. IMHO it makes the car noisier and feel mechanically less refined in town than my daughter's 75,000 Aygo and is totally at odds with the nature of the rest of the car.
Once in 5th gear the 'rattle' disappears but is replaced with a quiet high-pitched whine from the final-drive.
All of these noises are, I believe, normal for the up! and are probably not helped by the high levels of refinement and lack of other noises in the car. I am investigating the availability of a engine bay sound-deadening kit to see might help to take the edge off some of the gearbox noises.
Having said all this, overall I think the up! is a brilliant car and I I am generally very happy with it - for a City car it is so good in so many areas that it deserves the praise it has received. Which is good as I spend at least 2 hours a day in 5 days a week!