Anything that causes the frame rate to drop substantially is due to the graphics engine (as opposed to apparent slow down in the game logic, which is not reflected in the emulator's frame rate and is caused by CPU timing inaccuracy). The graphics engine frequently encounters a few common "problems":
1. Large polygons; especially on video hardware that doesn't perform too well to begin with or can just barely achieve 60 FPS in the first place. I think this might be due to the complexity of the fragment shaders creating some sort of fill-rate problem. On my development PCs, which cannot achieve anywhere close to 60 FPS on Daytona 2, the frame rate drops substantially -- sometimes by nearly a factor of 2 -- when the camera pans close to the vehicles in the attract mode sequences. Clearly not a geometry-related problem.
2. Too much geometry. I removed instrumentation code to keep track of the complexity of scenes a long time ago, so I don't know how much of a problem this really is. Generally, scenes aren't that complex by today's standards. I haven't checked, but this may be the cause of slowdown in the Star Wars trench scene and just before, when the tie fighters are descending into the trench. Model 3 has automatic geometry level-of-detail control, which usually isn't very important, but it's possible that it's being put to extensive use here. Supermodel always selects the most complex level of detail.
3. Texture uploads. Due to a bug in my caching algorithm somewhere, I play it safe each time a texture is uploaded and re-upload the entire 2048x2048 texture sheet (individual textures range from 32x32 to 512x512, and are usually somewhere in the middle of that range). Generally, games pre-load textures, but Step 2.x games often swap new ones in during game play. Daytona USA 2 and Sega Rally 2, for example, always do this in the same parts of the track.
3. Weird scene data. This is what's killing Harley, ECA, and Ocean Hunter, and it also seems to happen in Daytona 2 Power Edition in the desert segment of the advanced track. The scene database is a hierarchical structure that is traversed recursively and sometimes, infinite loops appear. Well-behaved games don't have more than a dozen or two levels of nesting, but some of the Step 2.x games have several hundred (almost certainly a problem with our current understanding of these structures).
Scenarios 2 and 3 are probably what you're seeing the most of.
If you play the Daytona 2:PE tracks in reverse (hold start during course selection, I think), you'll see that most of the geometry disappears. It's a scene database traversal problem.
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