Honestly, I'm disappointed. Shawn is pretty damn bland. There's very little about his character that's interesting. You've shown little to no likes, and no vices at all either. Honestly, he literally revolves around pokemon and the system. He's not a person, he's more like a robot.
Not to mention, he's stupid as hell. With the storage option, he doesn't need to settle for just a team of six, he can switch between pokemon freely. You could have been training some of the other ones in your storage like Raticate, Mankey, Sandshrew, Nidorino/Nidorina.
Then there's the levels. By time he left Viridian, Charmander was level 12. He only got to that level because he had a bit of a cheat in dragon dance, that let him beat evolved pokemon like Nidorino/Nidorina, Pidgeotto, Raticate and such, so why was Green's Squirtle just a level below? Does not compute mate. On top of that, Viridian Forest is large, very large, it would have taken him days to get through that. So why was he just reaching level 16 against Brock? That's stupid.
Writing Quality is decent I suppose, much better than the vast majority on this website. Sadly it doesn't even measure up to the average standard on Fanfiction.net, so 2/5.
Your update schedule is good, I'll give you that. So 4/5.
Story Development. You progressed along, but too much convenience, too many captures off screen, the quality of battles and such are subpar. 2/5.
Character Design. I already went into it above. 1/5.
You do a decent job with the World Background, well for someone on this website anyway. I'll just leave it at 3/5 because I'm feeling generous.
Overall, a 2,4/5 score. Not bad in my opinion since the vast majority of crap on this website shouldn't even rate a 1. You're at the point where you have potential and would benefit from getting constructive criticism on Fanfiction.net if you upload stories here.