Under the GS Window in Emulation Settings you can change the aspect ratio to either 4:3, 16:9, or Fit to Window/Screen. Using the Fit option will fit the entire screen on the PCSX2's current resolution (it can be changed, or you can hit the Maximize button to change it yourself).
Emulating the game is probably the better option if and only if you have a computer that can run these kinds of games easily. Getting the PC version will net you the best playing experience in terms of speed and what not (since it's not being emulated) but there's the down sides you mentioned.
I'd say emulate it but that choice is all yours bud.
Layin down enjoying the fun unleashing the power of the sun and capturing them all until I'm done.