NXengine works great, minor slowdown in pause/save menu. Also if you play with the retroarch menu it makes the sound all distorted.
BlargSnes works ok, DKC a little buggy, Chrono Trigger good, Secert of Mana good.
Gameyob works great, pknm Y is ok, missing sound effects, like pikachu growls.
Home Menu hax, works perfect, just change theme to a colour first, then install. If you change the theme at all, it uninstalls. make sure you use v1.2.
Quick NES great, Rygar actually runs smooth, simon's quest works great.
MGBA not great, can load PKNM LG, about 15 fps.
ft brony great, filezilla takes a little bit to connect.
prboom Doom awesome, can't bind certain buttons, but it runs great.
mednafen VB same as MGBA, jacks bros runs 8-14 fps, same as warioland.
Snes9x next slower than blargsnes
O3DS 10.1.0.27U
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o3DS is not the focus of development, but neither is the n3DS. The 3DS in general is the focus, as developers just want to get stuff working. The n3DS just happens to work better because that's what happens with more powerful components. It's really no different from PC development where rigs can range in power. I still remember some old DOS games that didn't have fps limiters, so as you played them on better rigs, the game itself became unplayable because everything ran too fast.
Once stability and compatibility have been finalized, then I'm sure performance will be looked at more thoroughly next. This is just the alpha stage. Don't forget that.
Read somewhere that the boot.3DSX can use 80% of the cpu on the N3DS, but can only access 30% on a O3DS
Limitations
At the moment, ninjhax only allows users to access 64MB of RAM, including on the New 3DS. This may change in the future.
While sound works on the New 3DS for homebrew running via ninjhax 2.0, at the time of the exploit's original release, there was no good way to use the DSP from homebrew, so sound output is not possible on the New 3DS using the old version. At the moment, there is also no known way of running code on the New 3DS's extra CPU cores under ninjhax, though it is possible to use 80% of the system core's time using
APT:SetApplicationCpuTimeLimit rather than 30% as was the case on the Old 3DS.
http://3dbrew.org/wiki/Ninjhax