Thats the nature of retroarch due to it having a overhead compared to a standalone emulator, as it has the whole UI running in the background while running games. It will also depend on system specs of course, throwing more power at the situation may make it fine in Retroarch as well. So a standalone will always have better performance, but that doesnt matter at all in 99% of cases as the emus generally are so easy to run.
I dont mess with 3DS emulation too much as i just use a hacked New 2DS XL, for that, but its still a fairly new emulator and lots of games still have issues, so its not a perfect experience in either case. Retroarch does add support for a stylus on the right stick as well as on the fly changing of how its displayed via controller hotkeys if thats something you want.