The slowdown seems to vary for people. For me, the game slowed down to at least 50% speed at around 50% text read and it becamse slower and slower. It seems to have something to do with your cache, where your profile is stored (usb/hdd/memory), whether the game is installed, and how big your profile is.
You should put your profile on the hdd, have the game installed to the hdd, clear system cache to minimize the slowdown. I had same problem with 11 Eyes Crossover and Root Double. Many people said they didn't experience the problem with 11 Eyes. Not too many people seem to have played Root Double for the full 1000G, so I'm not sure if that game is also just me having issues.