Hey, I had the same problem, but Pearl crashed when trying to look at Cresselia.
The way I fixed it was by loading the modified save file into PKHex, and I removed Cresselia's seen and caught check marks.
I then exported the save file, loaded the new save into PKHex and re-checked Cresselia.
I exported it a second time and when loading it on my 3DS, it doesn't crash anymore.
Hope this helps.