First Aid and Survival (Food). - In MGS3, if hurt, you would need to patch yourself up be it a gunshot wound or a broken bone etc. You would also require to hunt and eat to keep your stamina going.
MGS4 weapon modification - When it comes to weapon mod's MGS4 i feel was the best one out of the lot, although MGS5 weapon colour mods is a nice touch. I felt like i had more freedom to really customize my weapons on MGS4.
Jungle Theme - MGS3 is by far the best of the series, specially with its jungle theme, i feel like MGS5 is more like Red Dead Redemption.
Camping - As MGS5 is an open world with day and night, it would have been nice to even add a camp of some sort like RDR. That way you could maybe customize things that you could also do in the helicopter but not on the actual map.
Mother Base - I wish mother base was a little smaller and not as big as it was. Also it would have been nice to go inside it and even salute your fellow soldiers when they salute you.
Civilians and rebels - Maybe they should have added civilians or rebels. MGS4 had rebels on the first 2 acts, i would have been nice to see some extra action from time to time. If you help them, they could possibly help you. Civilians just going by doing there daily routine. Maybe try and save some of them who are being picked on by the enemy. If you help them, it could have added to your heroism points etc.
There are a few more things, is there anything else you would like to have seen in the game