I like quite a few things about the 5E Monster Manual.
But, there are a few minor things that I dislike:
1) Light blue colored background that has the equivalent of ink smears on it. It makes the pages look dirty. The light colored background in the PHB is similar, but the difference is black print on a contrasting color in the PHB and the "colored smears" are so feint as to hardly be noticeable. There are some pages where black on blue (or feint black smears) in the MM just make it more difficult for my old eyes to see the text. It's legible, but it's harder to see than it should be. I prefer to not have to squint a little in some places, just in order to read. I do not have this problem with the PHB.
Huh, not entirely sure what you're referring to here. Are you talking about when they have a table and highlight every other entry with blue? Or when they have a variant with a light colored background? I don't have the greatest eyesight by any means, but I haven't heard of anyone having much trouble reading the book.
2) No list of monsters by CR. There's a web printout, but it's annoying to have additional sheets stuck into your Monster Manual that will eventually be misplaced at just the wrong time. It's also supposed to be in the DMG, but until we get that, ... Like the spells not being segregated by level in the PHB, this just seems like a usability issue. If I go out of my house and want to set up some encounters, I now have to take two books.
I agree that this probably should have been included. It would have added only one or two additional pages if they spaced it right, and would have made a lot of people happier. However, I would argue that with bounded accuracy, getting the CR exactly right is far less of an issue, and making encounters should be based on the environment and what just seems fun to fight in general. I'm throwing four Mummy's at my level 10 party, and it's supposedly a hard encounter. But I can also see where they're going with putting it in the DM's guide, for exactly the reason you're complaining: if you are out and about and want to make an adventure, bring the DM's guide exclusively, and the Monster Manual wont matter until you're actually running the monsters.
3) No table of contents of the appendix creatures or of any of the specialized creatures (like a Blue Dragon). Again, a minor nit, but when the DM is going "where is the horse, where is the horse?" because it is not in alphabetical order. And the Index is partially a repeat of the Table of Contents, hence, waste of space. Sure, the exact page of a Black Dragon is listed in the Index, but it's not too hard to find a Black Dragon by looking under Dragon. The Index almost seems superfluous. So to find a Gargoyle, the DM can look in the easier to read (larger print and a single page) Table of Contents. To find a horse, the DM either has to know which appendix it is in, or go to the Index. The DM also has to know if it is a riding horse, or a warhorse. Horses do not exist. It just seems that they could have put the entire Index in the table of contents and been done with it.
Yeah I agree with this somewhat as well, especially in the case of things like winter wolves and wargs. These are monsters through and through, yet they're lumped in the "miscellaneous" category with the animals. The table of contents is supposed to be more of a summary than the index, but they do seem to have weird overlap that makes one superfluous.
4) The pages are wavy (i.e. if you close the book and view it sideways). Not a biggy, but just subpar for a brand new book. This might not be true of all MMs.
As others have said, this isn't a WotC problem, but a shipment problem. No way around it unfortunately.
5) I'm also not a fan of the "weird aura" artwork around creatures that most of the monsters have around them. It just detracts from the picture. Sure, there was some of this in the PHB, but not a lot. Here, it's practically every picture. It makes them look like good artwork superimposed on bad watercolors. I'm sure that some people love this, but meh.
I hadn't noticed until you pointed it out, but it does seem a little bit weird. I think what they were trying to do is make a pseudo background for those creatures that lack one. As you say, not a big issue, and a minor stylistic point.
So yeah, a few of these are pretty odd, but the biggest one to me is that they should have replaced the index of stat blocks with a list of monsters by type, specifically for when player characters try to summon something. It took me far too long to figure out that when a player wants to conjure an elemental they aren't limited to only elementals and can use anything of that type like mephits. Having to search through essentially the entire book to figure out which ones were which is something that could have been easily mitigated by a different type of index. Overall though? Probably my favorite monster manual of all time, minor issues aside. No book will be perfect, and I'm gladdened by the amount of work Wizards decided to put into this.