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.
There are 511.
I made the following spreadsheet, which might be of interest to somebody who wants to track their progress:
http://www.thunderpeel2001.com/GameFAQs/MGS2-Missions.xlsx
Top tip: These are some amazing tutorial videos by user "Dat Boi Treezy" for getting past the tougher levels, too: http://bit.ly/VirtuallyImpossible
Here's the complete list I put together:
RAIDEN
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 40
First Person View Mode x 5
Variety Mode x 7
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Hold-up Mode x 10
Photograph Mode x 6
Raiden Total = 103
RAIDEN (Ninja) (available when Raiden is 50% or higher)
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 5
Variety Mode x 1
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Raiden (Ninja) Total = 41
X RAIDEN (available when Raiden and Raiden (Ninja) are both 100%)
VR MISSIONS
Streaking Mode x 1
X Raiden Total = 1
SNAKE
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 40
First Person View Mode x 5
Variety Mode x 7
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Hold-up Mode x 10
Photograph Mode x 7
Snake Total = 104
PLISKIN (available when Snake is 50% or higher)
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 40
Variety Mode x 2
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Hold-up Mode x 10
Pliskin Total = 87
SNAKE (Tuxedo) (available when Snake and Pliskin are both 100%)
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 40
Variety Mode x 2
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Hold-up Mode x 10
Snake (Tuxedo) Total = 85
SNAKE (MGS1) (available when Snake (Tuxedo) is 100%)
VR MISSIONS
Sneaking - Sneaking x 10
Sneaking - Eliminate All x 10
Weapon Mode x 40
Variety Mode x 3
ALTERNATIVE MISSIONS
Bomb Disposal Mode x 5
Elimination Mode x 10
Hold-up Mode x 10
Snake (MGS1) Total = 88
Total VR Missions = 358
Total Alternative Missions = 153
Total Missions = 511
Best Answer
Unfortunately, there is no better way to aim.
This is due to lack of a feature called "Pressure sensitivity" in modern controllers. DualShock 2 and DualShock 3 used to have pressure sensitive buttons. Back in the old PS2 days in order to look down the sights, a player would have to lightly hold the fire button and fully press it when targeting is done. I assume the game developers had to change the scheme to match the modern controllers.
Also, you cannot move whilst in first-person view.