The installer automatically picks Program Files as install location. This is not advisable on Vista/Win7 as writing to Program Files requires admin privileges. By default install location should be C:\Games\FreeSpace2 as this is default in the FS2 installation. Total Conversions on the other hand either will package this with their downloads or have clear installation instructions.
This launcher is not intended or designed to be installed directly in the FS2 (or any other TC's) folder. This launcher is designed to be completely independent of the mod of FSO installed.
In the mod selection list, it is a bit annoying that infotext disappears when you select mod.
This certainly can be changed, it is mostly like this because when the list was designed there was not going to be enough room. Does anyone like the infotext disappearing when a mod is selected?
For some reason wxLauncher does not detect OpenAL and detect is grayed out.
Hmm, can you run the debug build (linked at the bottom of my original post) and post the log (instuctions for finding it in the Original post).
Another issue is that the launcher seems to think Windows reports 1 joystick with 3 or 4 plugged in. Old launcher only displays one. Calibrate button doesn't work for any of the four joysticks and they're all named as "Microsoft PC joystick driver", making it a wee bit harder to find the one that is actually my joystick.
Hmm, do you have any other controllers installed, like a game pad? In any case, as above I would need to see a log from a debug build.
And finally, profiles still doesn't seem to work. No matter what settings I tick, once I press "Play" the launcher uses default settings. None of the settings in mods, basic settings or advanced settings are used.
Hmm, can you also include the profile files. They are in the same folder as the log and are name pro*.ini.
Launcher doesn't seem to detect uniquely named fs2 open executables, only those that follow certain naming scheme. Didn't find a way to select differently named exes manually either.
Currently it will only enumerate executables that start with fs2_open. I was not aware of exes that are FSO that do not have that naming scheme. I will talk to kkmic about adding a way to add exes separately.
At that, I am aware that an executable named
fs2_open_includes.exe, for example, would be shown as just
FreeSpace Open Release. I need to adjust the filename parser so that any extra text in the file name would be shown in the list.
As I couldn't get the launcher to use any settings beyond very defaults, I'll let you know more feedback once these have been sorted out.
Okay, looking forward to the additional information as I am not sure what you are getting at here.
It seems that with this launcher I can no longer use fs2_open exe directly to fire up my games. I only used the old launcher when I needed to change mod folder or change a setting, other than that I always used fs2 open exe directly. Oh well, I'll adapt I think. 
Hmm, I will have to look into this because it is not supposed change anything in that regard.
If you're installing a program, installing to program files shouldn't be a big deal. Needing admin privs for that shouldn't be a problem. Subsequently writing data to that directory, however, is.
The only time the launcher should be have its folder written to is when it is being upgraded. Everything that this launcher writes is done to its folder in the users profile or to the TC's folder (fso_cmdline.cfg).