Metal Gear Solid series creator Hideo Kojima commented that when he gets asked "which title should I play first" (from the Metal Gear Solid The Legacy Collection) he answers "MGS 3." See the full quote below.
“When the concept of “Legacy Collection” was brought at mtg from sales team, dev side stated that it’d be hard for current user to play MGS1. Since it’s bird-eye view, you can’t really see the front side which makes it hard to self-adjust for someone accustomed to FPS/TPS.
“I often get asked “which title one should play if haven’t done MGS series?”. Play MGS3 as control is more modern, if you liked it then MGS4. MGS1+2 has camera w/ bird-eye view. If you want to learn the story, then just read the novel. I’d suggest [Peace Walker] for younger gen, but its hard to play solo unless you do Co-op w/ PSP/online. Hard boss battle if u like to take time and play.”
I couldn't agree more with Kojima. MGS 3 is a classic and in my opinion probably the best stealth / MGS game ever. If you haven't yet, check out the Metal Gear Solid The Legacy Collection. It includes all 8 MGS games and other bonus content.