This should be helpful for some of you.
Go to your installation folder (default: C:\Program Files\AeriaGames\MegaTen or C:\AeriaGames\MegaTen)
(if you can't find it, you have to open up the Setting
menu in the launcher, then click Apply
Replace it with your desired resolution.
Should work for any resolution (16:10 and 4:3) as long as your monitor and graphic card can handle it.