"I see what you mean, because if I just edit the rom to run faster, there will be a constant frameskip, which would be bad for some parts of the games."
But even your approach doesn't make much sense. What does the ROM have to do with frameskipping? Frameskipping generally referred to a way the *emulator* handles skipping the rendering/blitting of a single frame. For example on the Playstation, in simple terms that disc is pretty much a series of instructions which are read, then "emulated". By "emulating" these instructions, this is accomplished by methods using fancy terms like an interpreter and dynarec. Each of those instructions is processed and determined to be a certain opcode by the bit layout, and then converted to something the target platform (such as the PSP) can understand. All of this takes into consideration different ways of handling input, memory cards, storage, video, audio, etc.
If you edit the ROM you're probably going to see a series of instructions of a certain number of bits. For instance the PS1 is a 32bit platform and uses a 32bit length instruction.
Guessing you aren't changing the instructions, you're probably more concerned with the chunks of data, specifically the textures.
And from what you've said the textures should be converted to a type that the PSP natively understands, such as BGR555. If you go through all the trouble padding the difference in size of the textures, and making some sort of way of processing ROMs to make this easier to do...I have a feeling it won't go much faster.

...The textures are converted to a color layout the PSP understands, and then held in a cache (RAM) until the cache gets full and that texture eventually gets kicked out of RAM. If that texture is needed again it gets converted.
Wouldn't it be smart to see how often textures in the cache are being converted more than once, before going through with this?
If they are being converted way too much, it might be a good idea to look at the way the texture cache is handled, and see if you can squeeze more textures into the cache, or go about it a different way.
And if not that, and you do edit each ROM and etc...what does this have to do with frameskipping?
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