New launcher:
1) Asked me about data folder, I've guessed it is fgdata and I was right, please make it obvious in the launcher what folder should i select, this issue is probably related to my config and people who upgrade will see it too.
2) Default tab is always "settings", it does not remember my tab of choice. BTW: need more settings!

3) Aircraft tab: Height of the aircraft entries is fixed, but width of the image of an aircraft can be different and text is displaced a little to left or right, would be nice if pictures and text will be lined up/resized properly (height should be fixed as it is now).
4) I don't like Location tab at all (except runway selector - it is nice

5) When I exit from the game it won't go back to the launcher (kinda unusual)
In game:
6) My config from 3.4/3.5 was not loaded automatically by 3.6 so I've set up everything again (there was crash after exit with jetway errors, so I resetuped everything yet again because it lost my changes).
7) Red building bug is present (I've discussed it with Thorsten earlier): viewtopic.php?f=37&t=25472#p233349

9) Cessna is very nice, it has much bigger CHECKLIST with lots of different modes, when I open menu with them (list of entries like Before starting, Take off etc) it is too big for my 19" 5:4 (which has huge height already), it would be nice to have arrows to move from one checklist to another without that troublesome menu selection.
10) "Use point sprites for runway lights" - please make it automatic, if it is not working properly on ATI cards turn it off automatically! (please! on/off/auto)
11) When I switch with alt+tab between simulator and other programs flightgear will change its mouse behaviour (TAB key). Really annoying.
12) Is that popup in the middle of the screen about "cycling mouse behaviour" is really necessary? How i suppose to fly with it blocking my view!? Could you move it somewhere else? or disable at all?
13) Some airplanes will not work yet (like 707).
So far I like it, but those issues should be mitigated. Will continue to test it some more. I will post updates here.