Well, I'm not sure about the skin problem. Post that on Minecraft's website, Mojang.com and try tweeting Jeb about it. For Pixelmon, you can simply go to 'Profile' in the bottom left, the edit profile button, and change the version that says '1.6.4' to '1.6.2'
Update Java, make sure your not running tons of programs, and do this:
Right click on the taskbar > Open task manager > Go to 'Processes' > Right click on 'Javaw.exe' and 'Java.exe' > Set the priority of both as high or above normal.
Open the Minecraft Launcher > Press 'Edit profile' on the left > Go to the bottom and tick the box 'JVM Arguments' > Change the number next in the -Xmx1G Area to 2 or 3.
I can get up to 1k fps, and the F3 meter gives me abouyt a 50fps drop, but thats not hwat i'm on about. I'll try and record it and upload it, and it's not a MC bug, since Fraps and Dxtory show the same fps as the F3 mode.