Straight up, your pallet method sucks.
Try put all the reds in 1 row from lightest to darkest. You could compact your 6 rows to 4. One red, one yellow, one grey/white, and one separate column for just the blue. My pallet sheet that I made at school has just about all Kanto Pokemon, I did it my way and it looks and works alot better.
Your Team Aqua trainer... Whats with the hat!? Its so poofy! Should try scratching one or revamping and borrowing from an Aqua Grunt.
Your only things that I classify as "good" is your Color Swaps-- Very easy with proper pallet design
-- Banners, Heartful/Heartless, Advanced recolors and your cosplay was pretty funny.
Your trainer cards are funny... not in a good way. What is with the white pixels all over? Clean those off atleast! Bulbapedia has sprites, hit PrSc, paste on paint, clear on the back color, this way you wont get the missinng black outlines like lots of people do.
This post turned out longer tan I thought Lol.