Transfer Metal Gear Solid 3: Snake Eater Subsistence saves to PlayStation and unlock trophies

This can be done with the uLaunchELF browser. uLaunchELF is homebrew software, so must be run on a modded PS2 or via other methods for running unsigned software (the same techniques can be used to run pirated games, so I won't go into detail).

Once in the browser, copy your saves from mc0:/ or mc1:/ (the first and second memory card slots) and "psuPaste" them to mass:/. This will produce files which can be used with mymc to produce PCSX2-compatible memory card images.

The only "pro" for PS2 I can think of are better analog button controls for the PS2 version (the PS2 has analog controls on all buttons except start and select and this was supported in MGS2, specifically for aiming and perhaps for something else).

Other than that, I think the HD version will be the better choice, first of all is the HD aspect, meaning upscaled graphics, but also worth mentioning that included are the later version of both games, Substance for MGS2 and Subsistence for MGS3, which included extra content and in the case of MGS3, a new camera option (although some features some minor features which were included in Substance/Subsistence were removed from this HD version, as well as nightmare sequence which was available on the original Snake Eater). Also included in the package is the PSP game which wasn't available for either platform before.

In cocnclusion, I say the HD collection all the way.