Oh i'm not good at these rating things, but i'll try:
Title Screen: I like the title screen, it shows the title and the main pokemon Umbreon :)
Introduction Sequence: I liked it, but the picture of Pikachu and Cyndaquil sleeping isnt transparent, so the white background doesn't blend with the green one, you might want insert the copyright image into the start up screen, to replace the Enterbrain logo.
Oak introduction: Yet again I did not see anything wrong about this, except that I think you should change the Oak sprite to the FR/LG, or recolor/shade the G/S/C sprite to make it advanced style, same thing for Hiro and Sentret.
Hero Sprite: There's some black spots on the charset (while facing left or right, his pants are black at the bottom) that you might want to change, take reference to some FR sprites, and then fix it up.
Quality of graphics rips: Some of the rips had a bit bad quality, but I guess they got a bit screwed up, when you saved them(?), you just need to fix it and it will all be good.
Quality of charset rips: The ripped charsets had no problems as far as I could tell, except for Brawly, he was a bit screwed up.
Message system: Didnt lack anything really.
CMS: This had no problems but I think some of the pictures were a bit screwed up in quality like the other ripped ones.
CBS: I think there's been enough comments on this already, so i'll leave it out.
Map Design: It looked good, but there was some errors in Bantam Town, I noticed some of the trees was just copy/pasted onto some of the others, and that didnt look too good.
Story (even though there's not much yet): It's good, and it had Umbreon, one of my favorite eon, :)
Gameplay (running boots, etc): The running s***s were like in Pokemon, except for the picture of the boots, which didn't bother me.
Can't really rate the bike since it wasn't done yet, but the basics of it works.
Lag (too many events at one time?): It didn't lack for me, so I cant really say anything about this part.
OVERALL (score of 1-10): I give it a 7, with a few fixes here and there, it could be a definate 10 ;)
Hope this helped :)