So it sounds like the NPC portraits, combat backgrounds, and GUI panels are your own work? Does that include the enemy sprites? I don't really know what's stock RPG Maker. I didn't watch all 13 minutes straight through, but I got the highlights. On the whole I actually think it looks really good, but I do have some criticisms.
The portraits look great as far as I can tell. The hair and clothing especially are impressive. There are a few things that look a little weird to me: Eric's protruding teeth, the medics' very square faces, and Aana's just-a-little-too-big eyes (they're creepy), but maybe those are intentional.
The battle backgrounds also look really good, but I think they might be a little too detailed. The slimes blend in with the rocky ground and the blue dragonflies blend in with the grass. It's kind of distracting when the focus should be on the enemies. The enemy placement also looks a little strange in some places, such as at 8:15 when a slime appears to be floating above the ground.
It looks like there is a day/night cycle? Most of the video looks like it's at sunset or night, so I'm not sure what it looks like during the day. The night filter looks good, but the sunset filter might be a little strong as it washes everything out into a sepia. I wasn't sure at first if it was sunset, or a flashback, or if it just looked like that. Why does the battle at 2:31 temporarily change to daytime?
As for the GUI, the panels look good. I like the blue theme and angular highlights. I don't like the font (Arial italic?). It's very plain, but also hard to read. It also looks like there are multiple fonts in use? I would drop most of the italics and underlines and use one font as consistently as possible. The dungeon mode screen especially looks kinda bad, as it fills the screen with text of all different sizes. From an interface perspective I'm not even sure what's going on with that screen or what I'm supposed to do. The little text box at the bottom (e.g. at 12:45) also needs work - the two lines of text are too close together and the text runs out of the box. The use of fonts is actually my biggest complaint - if you clean this up, the whole game will look a lot more attractive.