I love Bestiaries, or should I say
well illustrated bestiaries. A list of statblocks does nothing for me. I want the pictures that go with the beast. Even a compilation of unusable monsters that are well illustrated has me buying the book.
I like bestiaries separated out from the main rules the way of the AD&D Monster Manual. Tucked away inside the core book makes it feel small and lost when I want my book of beasts to stand alone begging to be expanded with further volumes. Those beast expansions could be with settings Lamentations or just a book but they should be separated. In Veins of the Earth the monsters really informed the setting before you read about the place, that worked very well but Im a fan of DIY games and want the DM to be able to put together their own worlds and adventures so having them in their own bestiary (AD&D and Pathfinder style) is probably the preferred way most of the time .
What I haven't seen is an attempt to organize bestiaries in a useful way. That is typically a D&D or OSR bestiary will have Greek Myth (too many to name) mixed with a couple Asian beasts (Oni, Rakasha), and some outright inventions (Bulettes and Aboleth), none of which really go together. Then the next bestiary would do the same thing but a different hodge-dodge of beasts that don't belong together. This worked fine back in the day when they were making it up as they went along and included whatever they could think up, but now? Now we have the luxury of being able to plan. Piazo had the beasts all laid out for them when they planned out their bestiaries but didn't really do anything to reorganize. If you are making a sword & sorcery game why include Medusa (Crypts & Things)? If you are going for Grim Dark renaissance why include Elves and Dwarves (Lamentations of the Flame Princess)? The choice of beasts helps establish the setting and more thought should be put into the selection than just using the standard beasts found in every game mixed together in exactly the same way.
Another thing that bugs me, if you are going to go the hodge-dodge route, is that bestiaries tend to include all levels of beasts to cover adventure parties from first to 10th level (pretty much everyone does this). Basic and Expert D&D got this mostly right because of the nature of those games but everyone else sort of lumps them all together. Lumping them together means the DM has a limited changing selection throughout a parties career when it would be more useful for a DM to have more low-mid level monsters and a separate book from the high level monsters. I can't help but think this is a marketing decision as most folks probably play at lower levels but I don't know. I could be just everyone making bestiaries the way they'd always done so instead of trying to stand back and think about it.
The only bestiaries I can think of where they really shook things up and rethought things was 2E where they had those binders. The idea was ahead of its time. I hate the idea of using binders with the torn ring-holes and all, but the idea is perfect for the days of PDF where there are programs that allow you to pull apart one pdf and assemble another one could truly make a personalized bestiary, which brings me to my last problem.
The 2E bestiaries were designed with a beast per page. I like one beast per page, I don't like beasts sharing real-estate with other beasts. Yes this limits things when you come to beasts with limited info, but beasts can be combined with like beasts (all bears on the same page) in such cases, and if that doesn't work perhaps the beast needs to be rethought, what purpose does it serve. I like having enough gygaxian realism mixed with adventure hooks on each beast but I don't need an encyclopedia as I'm likely to toss those colorful bits anyway. Also, a problem with 2E is they included a beast on the back of the page. They had to, printing costs being what they are who would allow for blank pages. So if you liked on and hated the other well, suck it, make photocopies at a dime a piece. This is a problem that also goes away with PDF.
I think the problem really gets down to the compatibility of most monsters. You run a Lamentations game and you can use the Pathfinder bestiaries if you want with minimal fuss. Since most DM's probably have a vast assortment of bestiaries they don't really think about it and just pick from here or there but that doesn't mean the publishers shouldn't try a bit more.