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
Edit: Before you downvote this answer for being “link only”, please consider for a moment that it’s impossible for an answer to contain the contents of 48 videos!
Firstly, here's the complete breakdown of missions you will be facing in this final stage:
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
Total = 88 missions
Bonus: I've created a mission tracker so you can keep track of your overall progress through all 511 missions, too.
Unfortunately there are no general tips or tricks I can share. The missions themselves build upon everything the previous 423 missions have taught you. I could say that playing on XBox 360 is marginally easier due to its controller changes. And that hammering Triangle/Y is a good way to grab onto ledges. But it's mainly about taking that knowledge and skill you've developed up until this point and applying it. Sorry!
There are videos showing people completing these levels, but unfortunately they're usually people showing off their madskillz. Luckily there are a series of I've been able to find that explain how to complete each level in an easy-to-follow manner, without requiring patience-shattering super-skills.
(Credit to Ash Treezy (Dat Boi Treezy) for making them.)
I wish I could summarise their contents for this answer, but it's impossible. I used these videos to get the achievement myself on PS3 and XBox 360. They are easily the best resources I have found, official or unofficial.
VR Missions
SNEAKING
Sneaking 1
Sneaking 2 (same video as above - just further in)
Sneaking 3
Sneaking 4
Sneaking 5
Sneaking 6
Sneaking 7
Sneaking 8
Sneaking 9
Sneaking 10
ELIMINATE ALL
Eliminate All 1
Eliminate All 2
Eliminate All 3
Eliminate All 4
Eliminate All 5
Eliminate All 6
Eliminate All 7
Eliminate All 8
Eliminate All 9
Eliminate All 10
WEAPON MODE
VARIETY MODE
Variety 1
Variety 2
Variety 3
Alternative Missions
BOMB DISPOSAL
Bomb Disposal 1
Bomb Disposal 2
Bomb Disposal 3
Bomb Disposal 4
Bomb Disposal 5
ELIMINATION
Elimination 1
Elimination 2
Elimination 3
Elimination 4
Elimination 5
Elimination 6
Elimination 7
Elimination 8
Elimination 9
Elimination 10
HOLD-UP
Hold-up 1
Hold-up 2
Hold-up 3
Hold-up 4
Hold-up 5
Hold-up 6
Hold-up 7
Hold-up 8
Hold-up 9
Hold-up 10