I have never played a Metal Gear game but when I picked up Metal Gear Solid: Snake Eater 3D, I realized that this was DEFINITELY worth the wait!
This game is the first game story-wise, which takes place in 1964 where you are about to commence the Virtuous Mission. Upon descent, Snake makes it to the target, tries to extract him, and shit goes down from there.
To start with, the visuals are superb in this game which really showed that Konami didn't want to make this game just a port of the PS2 version. Another good thing is the epic story-line which had the James Bond feel to it with the main theme Snake Eater, the inclusion of a hot woman (EVA) all the sneaking around you had to do and the occasional humor from the characters. the epic cutscenes will also stay with me, specifically the scene where Ocelot shows his gun juggling skills in style! Too bad some of them are dampened by the really bad framerate due to hardware limitations. The game will offer a Circle Pad Pro option, but I had no problem with the control scheme without the Circle Pad Pro, as the controls seem to work really well on the 3DS.
The only occurring problems are the frame rate is inconsistent and the lack of modes compared to the Subsistence/HD edition of MGS3, which had the Secret Theater, or even fully playable versions of the MSX Metal Gear games. There will be slowdown on certain areas like when there's a lot going on in a cutscene, which is a shame that they did not fix that.
If you do not own a PlayStation/Xbox and want to play a Metal Gear game on the go, MGS3D is the way to go. Otherwise, I fully recommend you buy it on the MGS HD Collection or get the actual PS2 copy of MGS3 whether it be the original or Subsistence.