cell9 has released a plugin for the New 3DS which allows you to configure the CPU Clock, which improves performance on older titles, here is a quote from the source:
It was recently found that New3DS's CPU clock runs at 804MHz when running system menu or playing New3DS-only titles (i.e. Xenoblade), which is about 3x faster then Old3DS.
However, when running games for old3ds, New3DS will set its clock-rate to 268MHz and disable the additional 2MB L2 cache to simulate the Old3DS's behaviors.
This plugin allows you configure the cpu clock rate and enable the additional L2 cache, which could improve the performance of Old3DS titles running on New3DS hardware. From a simple test, the MGS3 game was more than 2x faster on loading scenes.
I haven't test this plugin on other games, please tell me if you have tried it.
Copy cpuclock.plg to /plugin/home in the sdcard.
Boot NTR and start the game, after the Nintendo 3DS logo disappeared and game screen was displayed, choose the 'CPU Clock' item in NTR Menu.
Select the last configure for the best performance, the first one is the default configure for running Old3DS titles.