Plotwise and fan service-wise I think MPO did a way better job than PW or MGSV in closing in the gap between MGS3 and MG. MPO actually adresses parties that metter in the overall story (FOX, CIA, Pentagon, Patriots, Fox-Hound, mentions outer heaven), where PW and MGSV diverge from the “main story” with uninteresting parties(MSF, XOF, Diamond Dogs, Cypher).
MPO adresses the cration of fox-hound (long date important facction within the MGS lore) and the begining of the friendship between campbell (iconic charismatic character) and big boss, even how they met! PW brings Miller out of nowhere! He simply is there and he is your friend and second in comand. The game just throw that on you and you have to accept that and play along. You didn´t saw or took part in how Big Boss met Miller. PW and MGSV both adresses the creation of MSF and Diamond Dogs. MSF can be considered the bare bones of outer heaven but why DD after that? Makes no sense! I mean only if you are not the real big boss and he is actually creating outer heaven while you play this stupid game that has nothing to do with anything but being a filler.
The presence of Gray Fox (Null)(even if it seams a bit forced to begging with) and a rogue Fox unit (a galery of vilains worthy of the metal gear franshise). Characters like Python that had backstory with Snake that we didn´t know of.. but we buy into it because it´s well done. PW brings generic futuristic mechas as villains. No charisma there and most of them look to modern for 1970s considering the fact that in 2005 MG Rex was the top of the line. MGSV has a handfull of super-soldiers that looks like the frogs from MGS4 even in the way they are freakysh and the way they jump around. The only good vilains here are the ones that come from other games in the franshise but even so here they are poorly developed or missused. Like the anticlimatic Volgin reveal and than not even a final boss fight! Skull Face and XOF looks like what they are.. a antagonist force created solely for this game. None of the backstory of XOF or Skull Face knowing Snake, none of this makes sense. I don´t buy it. It looks too much crafted for this ocasion. It´s not something that we can believe it was there before. It just feels convoluted for it´s own sake.
In MPO Snake speaks! A lot! he is a leader! he has charisma! (something that David put into it very well.. also as a voice actor and script writter he did know and cared about the story. I doubt Keiffer could ever fill those shoes.) In PW snake is a mess following a ghost of the boss. In MGSV he is actually the ghost himself. The character has no charisma, no presence but it actually makes sense since he is not the true Big Boss... what feels as yet another of the famous Kojima´s bitch-slaps into our faces.
About the mother base concept, it was MPO who introduced it. PW and MGSV may have done some improvements on it but they missed the most fun and unique feature from MPO´s unit system. The fact that you could recruit the enemy bosses! if you take them out non-lethally you could recruit them and latter play as them! Something you can not do since PW and MGSV don´t have bosses. In MPO you could play as Python or Null as you played through the story mode! In MGSV you can´t play as Quiet or Ocelot even thought they are amongst your ranks. Even thought Ocelot will be playable on the online mode. Anyways...
I really believe that Kojima got pissed that he didn´t direct MPO and the people who did, actually did a hell of a job! Than he tryied to hard on PW. The boss´s AI? LOL how desperate and sheap!