It was hinted in MGS3 that Ocelot was the son of The Boss & The Sorrow or didnt some of you notice. This explains why a dead Liquid Snake can get into his head. Ocelot is a medium just like his father was.

Big Boss was always portray as the "good guy all along character" that was kinda the whole point of MGS3. Big Boss comes to realise when he sees how the US shafted The Boss that good & evil are not objective but subjective. The Boss' speak to Big Boss before you fight her in MGS3 explains my point.

However I do think that Kojima is guilty of 3rd degree retconning & should probably be kicked really hard in the groin for it. Maybe he should play through all his old games again before he makes MGS5.

Just to warn you all The Les Enfrant Terribles project include 7 or 8 clones of Big Boss so don't get get too pissed if you all see Liquidus Snake or In Need Of Defrosting Snake in the future. If memory serves me right Liquid was full sure in MGS1 that he and Snake were Big Boss' only surviving clones but then we got Solidus.