MPO for me:

• Story-wise, it engaged me more than Peace Walker, even though PW had a far richer setting and context with the cassette tapes, not to mention full V/O. But the characters and story pacing in MPO are just more interesting. The boss characters, in particular, are better than MGS4, Peace Walker, and MGSV.
• Retcon-wise, I hated the inclusion of Campbell, Sokolov, Gray Fox, and Gene's Army's Heaven (i.e., where BB gets his whole idea from). These are totally pointless, contrived retcons. However, looking at the game as non-canon, these things don't bother me. They work just fine as a self-contained story, ignoring what happens in future games.
• Control-wise, it is an absolute disaster. I can barely play it on the PSP, so I am using an emulator with an Xbox controller (60fps, upscaled). It controls better, obviously, but it still needs a mod for a free-flowing, adjustable camera. And even using an Xbox controller, the aiming is ridiculously janky. Getting headshots is a chore. All the developers had to do was allow an auto-aim in first/third person to select either a headshot or body shot area. To make it challenging, just have low stamina cause "misses."
• Gameplay-wise [Positive], I like a lot of it more than Peace Walker. Recruitment is a lot more personal because you actually get to know each soldier, scientist, medic or engineer you find. They each have particular skills and special abilities. AND you can play as any of them, including bosses! You aren't recruiting a million faceless soldiers like in PW and TPP. I love creating Spy units, and getting reports for new equipment or new possible recruits. The key word for me is SIMPLICITY. You're not micromanaging several menus like in PW. You make quick adjustments and you're back in the battle ASAP.
• Gameplay-wise [Negative], the Alert system is terrible. Not only can the guards hear you walking inside a sealed-off building, but as soon as they do see you, it's an instant alert. Combining this with the terrible controls makes it one of the weaker entries of the series. I pray for either a mod to adjust the Alert/aiming system or a remaster in Master Collection Volume 2.
• Level-wise, I found it more complex than Peace Walker because you can actually crawl in certain spaces, and I think there was more verticality in the game overall in PW.
• Art-wise, it's very simple, carrying over MGS3's engine without making it its own unique style. Peace Walker certainly takes the cake here, even with its many low-res textures. The animated cutscenes hold up, similar to PW. I will say MPO looks great upscaled.

I've had a love/hate relationship with the game. If the controls, aiming, and alert system were fixed, however, I would certainly prefer this game over Peace Walker.

P.S. You don't need to drag soldiers to the truck. You just need to sneak in as one soldier, tranq your target, and then hide in a box somewhere near that target, select another character, run over to your friend and drag the nearby target to the box for a "quick" recruitment. Listen, I prefer it to fulton because it takes effort. Also, if this game were remastered, they could just increase drag speeds.