I haven't done so in a while, but I like to post Linux Wine results for games I own. I didn't see a similar topic, but I've spent a little time with YS and figured I would put the experience out there.

I'm pretty sold on using Play on Linux to help manage things and to put games into their own environments. It also makes it easy to cycle through different wine versions if you need to. This is all the long way around saying I was using POL if that matters to anyone.

My results so far are very positive. I've primarily focused on YS1 but YS2 seems to be similarly successful (with a small caveat).

For the most part the game appears to function in full, without any strange behaviors, or bugs. YS2 does seem to have a few white pixels that don't fade away during screen fades. If you can live with that then I can say it otherwise seems solid during gameplay.

Game pad support: I'm using a 360 controller and it's working just great for the game. They rarely work, but in this case they do and it's and excellent fit for the game.

Issue with movies: The one thing that does fail seem to be what I think are movies based on the error that is created. When I start a new game I get a popup with an error. The good news is clicking the button lets me skip past whatever it is and get into the game which runs great from then on. The bad news is I have no idea what is being missed, and I haven't played enough of the game to know if there are other movies as you go through the game. It's possible that installing additional components could fix the movie issue, but I haven't identified them as of yet. If anyone does please add it to the thread.

Installer errors: I also got some errors as the installers finished. I just clicked through them. The installer seem to thing the installs went OK and the games launch without issue.

It should be noted that the results here are only for YS1 & 2 running on the 2D engine. The later games running in 3D will need to be evaluated separately.

My setup is as follows
Mint 17
Wine version 1.7.34-CSMT 64-bit
No additional components installed

If you open the configuration program, there is an option to disable movie playback entirely, which should prevent the error.
Also, my Logitech Precision Gamepad works with all the Ys games I've played.

Oath in Felghana and Origin also work well. The area/boss names in the upper left corner in Origin doesn't show up on my computer. In Felgana, the combo counter in the upper (not sure whether left or right) doesn't show up, but that's not a big deal, as it's also displayed in the lower left. Origin can run out of memory (especially if you are looking at the bestiary or play a full boss rush), but some people report that happening on Windows as well.

Unfortunately, the movies don't work on my setup either.

My setup is as follows:
Debian Jessie chroot (a bit out of date), Gentoo host
Wine version 1.6.2
Some additional components installed (enough to get Elminage Gothic to work).

edit: one more thing: in Oath in Felghana, I have sometimes seen glowing squares on the ground when there are projectiles around.

May I ask what you installed to get Elminage Gothic working? I've had some difficulty getting it to run on WINE.

Apparently, the game uses the same (or at least similar) engine as Agarest: Generations of War, and the WineHQ page suggests running "winetricks wmp10 xact devenum directx9". Note that wmp10 is there simply to allow the opening video to run so you can get pas it.

Anyway, have fun with Elminage Gothic! Note that if you are coming directly from a fast-paced game like a typical Ys game, it may take a bit to adjust to Elminage's slower pace.

the failur is certainly an inability to play the movies, but it's not a terrible drawback, because every movie it's a single file on the installation, they are simple mpeg (except for the extension) so any player should read them.
they are named like: ys1_opwn.dat ys1_rean.dat ys1_roda01.dat et simila. there are 2/3 copies for each one, from the different versions of the game.

one it's the intro video, other are likely a bit more into the game, or ending movies

there are not many and few that contain vital information i think

i wasn't able to find a way to make the game play them, bot quark and wmp9 aren't enough, and i don't know what other dll to try, but as said before it's not a big problem.

This is an old post, but I figured I should post my setup that works for getting all Falcom games running perfectly under WINE.

The overrides I have are amstream, dsound, gdiplus, quartz, and dmusic. I also have winegstreamer set to default to native, and I winetricked xvid.

I've tested every Falcom game released on Steam/GOG - and that setup should work for all of them. The last problem I had was with the latest Trails in the Sky update - and its' sequel. I had to implement my xvid overide then.