Very simple frame skipping code!

[gid15]

I think the heavy functions in the OpenGL pipeline are the PRIM, BEZIER, SPLINE and the frame buffer transfer command (XKICK if I remember correctly). The other ones aren't very time consuming.

Yes, PRIM, BEZIER and SPLINE can be skipped, but TRXKICK should not: it is used by some games to copy parts of the display list.
Also, bounding boxes can probably be skipped as well: skip BBOX and always take the jump in BJUMP.

Also I don't know if it is possible to use a profiler to check where exactly is the heavy rendering part, it would help a lot.

Statistics (e.g. duration of each VideoEngine command) can be activated by setting jpcsp.util.DurationStatistics.collectStatistics to true. Statistics are then displayed in the log file when Jpcsp exits.

In your draft implementation, you were actually not skipping any frame rendering: the GE list was still enqueued in the VideoEngine, the list processing was just delayed (probably to the next VSYNC). This would probably only cause the application to run slower, but not skip any frame.
The approach proposed by Orphis is much more promising.