Okay, so after a bit of testing, here are my thoughts on PicoDrive vs GenesisPlusGX.
PicoDrive did not run full speed with hardly anything.
Master System: Inconsistent performance, drops frames, has speed up/slow down issues and has sound pops. Of course, no FM sound support either.
Genesis: Seemed to have issues with PAL games similar to the GenPlusGX emulator. Alien Soldier sounded bad and played too fast, but also dropped frames. NTSC games seemed inconsistent as well with sound pops and inconsistent frames.
SegaCD: This played slightly better than GenPlusGX. There were minimal sound pops -- a few in the BIOS, but I did not notice performance issues in the games I tried. Heart of the Alien was selectable which for some reason does not seem to be selectable with GenPlusGX. No CHD format support.
32x: Playable, but with sound pops and some frame drops.
Game Gear: No support
SG-1000: No support
Genesis Plus GX in my opinion seems to be the emulator of choice for now.
Master System: runs solid with consistent framerates and FM sound support.
Genesis: solid emulation for NTSC games, but sound issues with PAL since it's forcing 60Hz.
SegaCD: Some slowdowns, especially in the BIOS, but most games run fine. Secret of Monkey Island has a lot of sound pops. Road Rash, Soul Star, Snatcher, and most other games run great. Heart of the Alien is not selectable from the first in-game menu -- for some reason I can only choose Out of this World. Supports CHD files so less disk space is used, due to compression, and less clutter with having only one file instead of multiples for bin/cue.
32x: No support
Game Gear: Solid emulation with consistent framerates.
SG-1000: Solid emulation with consistent framerates. Color palette seems accurate which is an issue with some other emulators.
We just need the emulation improvements given to GenPlusGX on the Legends Flashback for our Genesis/Megadrive Flashbacks.
I expected much better from PicoDrive. It's the only Genesis emulator that runs full speed on the old 3DS. It runs SegaCD games great on a New 3DS, so I thought it would run even better on this hardware. I don't know why, but the only thing it did well on my Flashback was SegaCD. I seriously think even last year's emulator was better than this PicoDrive... much better... seriously.