Hopefully this will give confidence to people that are contemplating the change as well.
Firstly the upgrade to 10 went very smoothly, the only issue that I found was that the install prep seemed to hang until I closed down Daemon Tools lite. I should say that it seems to pause for a long time in several places but at this point it hung for over 20 mins.
Once the upgrade was finished I went about trying to get various things to work that seemed not, like drag and drop into VLC and Everything (search proggy) not starting. In these majority of cases it was the fact that 'Run this program as an administrator' was set. If you switch off the UAC, which I do, then having apps set to run under admin causes problems when it didn't under 7. For example I run VLC from RocketDock. Both had admin switched on and drag and drag would not work for VLC and neither could you drag and drop apps into RocketDock.
So a general 10 tip if drag and drop does not work try switching off the admin user for that proggy and see if that fixes your issue.
Once I sorted out my issues and made the gui look less gopping I started work on FS9.
Now and absolute pre-requisite for it to work is that you must be using the FS9 NoCD patch that has been around for years. Make sure you are using the correct one for your version of FS9 (FS9 or FS9.1). This is because MS have automatically disabled some CD based software security which afflicts even there own products

I run FS9 in windowed mode so I didn't have any issues of a black screen on load. IF you use full screen mode normally I would recommend that you switch to and save in windowed mode before you begin. There have been numerous reports of black screens when the proggy is started and you have to switch to windowed to see anything. I should say that I have not checked on my system if this is the case or if there has been any permanent fixes. This is about getting it running. Fannying around is something to be done later.
I started FS9 using the FS9CPU_4CPU.exe proggy. and it took some time to start to load, i.e. greater than 0%, so I am guessing that somethings were being altered in the background for FS9. I did get a requester to install Direct Draw which I clicked on so I am guessing that this is not part of the new OS. It installed itself and the loading continued fine.
What I did notice was that the jaggies that I had eliminated from FS9 were there. This was undoubtedly due to the new Windows 10 nvidia driver I was using so I went and loaded my override profile for FS9 through Nvidia Inspector. No difference.
I tried to fallback to my last drivers but it failed the nvidia check as they were not Windows 10.
After some head scratching I eventually found that nvidia had renamed the FS9 profile. It was originally called 'MS Flight Simulator 2004' but is now called 'Microsoft Flight Simulator 2004' so I had two profiles and it was picking up the default one.
So I simply took a copy of the FS9 profile and renamed the internal ProfileName to 'Microsoft Flight Simulator 2004'.
This was then loaded and hey presto the jaggies have gone. Sorry to those with Radeon cards I don't know how to fix the jaggies on those.
So with a few simple planning steps it is easy enough to A) upgrade to 10 and B) get FS9 running.
Hope this helps.