I wonder if it's a bit to zoomed out? It just seems like there's too much space in the window.
We kind of felt that way with our Mario game on RMXP, so we ended up making everything 1.5x larger. Especially since your game looks somewhat like Mother 3/Pokemon Gen 3 (both of which were on the small screened GBA) it comes off as little jarring.
But I guess that doesn't really matter, heh.