PC's can't play all PS2 games perfectly. That is because the software is not optimized. Without all hardware and firmware details it's impossible to create a perfect emulator regardless of how powerful the host machine is. Even SNES and GBA emulation have a couple problems because of that. Some games that are well understood can run perfectly
The base 3DS has 2 cores and 4 times the RAM, along with 50% more VRAM. The New 3DS has 4 cores and 8 times the ram, with 150% more VRAM. 3DS just has higher quality shaders. Think of it as DirectX7 PS2 vs DirectX9 3DS, also the specs of PS2 was like that considering the prices of tech back then. ED4am.