Well, if you could notice frame drops, then perhaps your computer can't handle it?
What I meant by frame skipping, if I could recall the conversation properly, is something like vblank interrupting the frames. Vblank normally occurs for fishing (if I'm not mistaken), however emulators might insert a vblank when it's not supposed to.
The most obvious one would be stationaries: AFAIK they should only be Method 1, and a wrong vblank would make them other methods, thus illegal.
And no, the mon won't always come with a legal PID spread. It depends on what mon you encounter and how.
An example from someone who knows better:
(Context, the response was to someone asking about Pokemon Boxes' emulator. But the whole vblank business applies here)
and
Anyhow, if you don't wanna deal with it, just play on real hardware. :3