Xbox – Metal Gear Solid 3 HD: Didn’t get Fire camo

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.

According to this trophy guide:

[...] To earn the title MARKHOR you must collect all 48 different types of animal and plant life. That is all Snakes, Birds, Fruit, Mushrooms, Fish, Frogs and various other non-specific flora/fauna. You do not need to eat, just hold all 48 items in your inventory at least once in a single playthrough [...]

So, to answer your question, you do have to collect all animals/plants on a single playthorugh, but you don't have to eat them all.