People are harping about how Mission 46 just pops out of nowhere and it goes, "welp, that's the end". There's literally no build-up to it. 43 to 46 is just a jumbled mess. You kill a bunch of your men in the quarantine facility, the famous ashes scene happens and then (if you don't take the Butterfly emblem off) it jumps straight to 46 where you're in the hospital again. It is not a good transition at all, right there between 46 and 43 is clearly missing content.
Then there's the fact that Code Talker says, "Eyes on Kazuhira" implying there's something fishy going on with him that doesn't get resolved at all. And we already know Mission 51 got cut so Eli and Mantis go unresolved (officially). And there's still some other MB stuff I'm likely forgetting that went unresolved as well.
Quiet's mission even likely comes too soon as well as, again, it doesn't lead into 46 at all. They clearly cut a lot of build-up/pacing missions that lead to 46 and then the aftermath of 46 is Eli's stuff.
The way I see it, Chapter 2 would have been something like:
43
44 - Some mission goes here that builds upon what 43 set up
45 - Continues
46 - Continues
47 - Continues
48 - Something happens with Kaz here (or after completing 48 or maybe this is where Quiet's mission goes)
49 - Do a mission here to resolve Kaz (maybe this hints towards you not being the real BB)
50 - Truth
51 - Eli
And if there was intended to be a chapter 3, then it would be 51 is the start of Eli's stuff and it goes to about 55 or 60 with the last mission being what we saw in the CE.
43 to 46 is not paced right and to be honest, neither is the entirety of Chapter 2. A lot was definitely cut, no question about it. Especially when you can just complete side-ops to advance the story after you've completed one of the new story missions on offer.
