I didn't like 3 at first due to how different it was but it definitely grew on me and the hunting aspects gave it a different dimension.
2 was pretty good (best storyline imo) but I remember how fuming I was at the time that you played with Raiden for the majority instead of Snake. Think the developers were shocked by the backlash of it as they didn't make that mistake again
1 was just epic in so many ways. Obviously nostalgia plays a part as I was still really young then but I remember being utterly amazed when I realised to beat the psychic boss you had to plug your controller into port 2. Ahead of its time as I say.
**** it I was still umming and ahhing about this but thinking through it in detail has made me take the plunge and order it.