Well, I'm using the 3dfx plugin, and it doesn't even do that swirly thing. It just blacks the screen and goes straight into the fight :}
No biggie, but it works nice. I'm sure if I had a half decent video card the swirls wouldn't be THAT slow :}
Try this: In the configuration screen for Lewpy's Plugin, go to the "Off-Screen Drawing" section, and
set it to use "Extra+FBR". Then, under the "Framebuffer Access" Section,
select the "Write" option.
I can get a Voodoo3 to do the swirl stuff that's in FF9 to run at what appears to be 55-60fps, as long as the CD-ROM drive doesn't need to spin back up (since that's introducing lag caused by the drive, because the emu is designed to wait until the drive is back up to speed, so it halts). But, other than waiting on the drive, it's practically smooth as silk, the swirly-screen.
Now, I haven't tested how well FF7 would work with those settings, but they were
implemented for FF swirly-screen emulation in mind, so they are worth trying.
Oh, and one more important thing:
Leave Frame Skipping OFF for this! Frame skipping seems to conflict in functionality with what these settings do. Believe me, the Framebuffer effects will run faster/smoother with frame skipping OFF.