Emulation is more processor intensive than playing natively programmed software.
For example, Batman Arkham City runs perfectly on my PC, whereas Ratchet and Clank, an early PS2 game, can't get over 40 or 30 fps, the sound is slow, and the graphics look like garbage unless the Graphic Plugin is in Software mode, which disables the ability to use custom resolutions. But on the flipside, Persona 4 runs almost perfectly in a custom resolution, only problems are the sound hiccuping when the framerate bounces above the... 59.94 limit (I don't get that PCSX2... why not 60?)