Yes, the emulator is by me and Lordus. I do the core while he does everything to port it to Android, user interface, and so on (and license stuff)
Of course, not all games have the same demands and it can vary by a factor of more than 4 from least demanding to most demanding, but even 2D games usually use the 3D capabilities of the DS heavily.
I talked to Lordus and he says that Dragon Quest VI runs at about 130-140% on his Galaxy S3, which has quad 1.4GHz Cortex-A9s (GPU speed doesn't really matter). The Tegra 3 in Nexus 7 2012 is a little slower, but I'd expect it'd still usually be over fullspeed, although I wouldn't recommend running it with auto frameskip off. So this performance definitely seems a lot worse than it should be. There are a few possible things I can think of trying:
- Increase the audio latency setting. Normally this isn't something that should get better with frameskip, but I can't rule it.
- If you have a Bluetooth audio device paired those are known to sometimes make the latency even worse, so try disabling Bluetooth.
- There's an issue with Qualcomm SoCs in Lollipop where some texture uploads cause big stalls sometimes, which goes away if you use the 16-bit output option (slight quality degradation of 1 bit lost on red and blue). That shouldn't apply here, but it's worth trying.
- Make sure there isn't something else running in the background sucking up CPU time. Maybe using an app like this?
https://play.google.com/store/apps/details?id=com.bigbro.ProcessProfiler&hl=en
- Make sure that the device isn't put into an efficiency/power save mode that prevents it from clocking very high. An app like CPU-Z can check current clock speeds.
Normally, the device will thread 3D rendering on two or three cores if it can, so more than one core will be used a fair amount regardless of whether or not the threaded 3D option is set (which can cause further issues since it isn't really emulating things correctly)
To try to narrow down what's going try enabling the framerate display and see if it's erratic. If you have a sudden huge performance spike the auto-frameskip may spend a while trying to make up for lost time.