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Honestly, modern diversity is pretty good and you ought to get your head around how modern animals work before going into the fossil organisms where a lot of the anatomy is pretty speculative. I can speak to vertebrate morphology much better than invertebrate morphology, so my recommendations will focus on that.

1. A good dissection guide would help a lot. Personally, I like the De Iuliis & Pulera guide. It's well-illustrated and pretty generally clear.
   
   
2. Second thing you need is some reference material on biomechanics and general vertebrate morphology. There are a lot of vertebrate morphology textbooks out there, the Bemis text is probably fine for your purposes. A more specialized text on functional morphology (e.g. this one) would probably help a lot as well.
   
   
3. For fossil stuff, the best textbook surveying fossil morphology of vertebrates is probably the Carroll text, but it is incomplete for a lot of taxa. I really like the Gregory text on fish skulls, for example, which may fill in some of the gaps that Carroll leaves out.
   
   Finally, Stuart Sumida is a vertebrate paleontologist and functional morphologist who periodically consults with Disney and other major animation studios on animal & human locomotion. He's part of the reason there's a sea-change in animal (and human) animation quality in Disney films from Lion King onwards. He's got a bunch of animation resources here and periodically offers workshops for animators. His slides are mostly pretty text-sparse but there may be something of use in there.

I actually just searched for this sub with this exact question in mind! However I was thinking of something that introduced species chronologically, (i.e. starts with the messy buggers in the pre-cambrian, and works it's way through as much as we know).

Basically sparked by reading up on saber-toothed cats and finding out they're not actually Felidae, and I realised that while I absolutely love reading about pre-historic life, I really don't have much basis in knowing fully the various branches of life that have existed. Convergent evolution is amazing to read about, but so is evolution itself!

Just wish-listed these three books (1, 2, 3) on amazon, wondering if anyone could recommend if any of those might be what I'm looking for in terms of prehistoric life overall (and not just dinosaurs, though dinosaurs are obviously super cool too) but also possibly recommend any, as I know these are very broad overview encyclopedia's with pretty pictures. Don't mind detail and complexity, but not that interested in the process of excavations and such as it relates to palaeontology.

This is what I would recommend:

http://www.amazon.com/Terrestrial-Ecosystems-Through-Time-Evolutionary/dp/0226041557

It's 20 years old, but still good. This is based from the Smithsonian, they have a terrestrial ecosystem working group there and this was a publication by them. Check out the table of contents, it covers what you're interested in pretty closely.

It gives an overview of the problems, as well as how we know what we know, and a lot of detail as well into what was going on through time.

There has certainly been plenty of follow up work since then, but that's fairly easy to find with a literature search.

A recent good book is End of the Megafauna by Ross MacPhee, which examines the disappearance of most of the great beasts of the Cenozoic.

Two recent picture-heavy books: the Princeton Field Guide to Prehistoric Mammals and National Geographic: Prehistoric Mammals. The second is aimed at a younger audience but still has plenty of meat for adult readers.

Speaking of younger readers, John Rafferty's The Cenozoic Era: Age of Mammals will give you a good grounding in the geological history of the Cenozoic and what was happening around the world. It's aimed at high school and college students but doesn't at all talk down. Definitely worth the read.

Horned Armadillos and Rafting Monkeys is a deep dive on the isolated fauna of Cenozoic South America.

For a better sense of the actual fossil record, see Bruce Stinchcomb's photo-heavy Cenozoic Fossils books for the Paleogene and the Neogene.

This book: https://www.amazon.com/gp/product/0375824197?ie=UTF8&tag=laelaps-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0375824197

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The author, Tom Holtz, is honestly one of the most enthusiastic people in the field and this is a book that can grow with your son.

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https://www.amazon.com/gp/product/0142411930?ie=UTF8&tag=laelaps-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=0142411930

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This one is aimed at slightly younger audiences (squarely at the 8 year old demographic, actually) and is full of the sorts of facts and stuff that kids love to trot out when talking to grownups.

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Another thing I would recommend is, before you go to the museum, try get in touch with the curators or somebody in charge of outreach programs. We're all busy people but most of us are willing to take a moment out of our day to show a kid around behind the scenes, and if there's an active docent program at the museum you can also get a special tour of front of house stuff too.

Here's some good books about Pleistocene Megafauna:

Pleistocene Mammals of Europe is really good but a bit old.

Amazon Link: https://www.amazon.com/gp/aw/d/0202309533/ref=mp_s_a_1_1?ie=UTF8&qid=1500182591&sr=8-1&pi=AC_SX236_SY340_FMwebp_QL65&keywords=pleistocene+mammals+of+europe

Quaternary Extinctions: A Prehistoric Revolution is really good but it's some serious reading

Amazon Link: https://www.amazon.com/gp/aw/d/0816511004/ref=mp_s_a_1_1?ie=UTF8&qid=1500183028&sr=8-1&pi=AC_SX236_SY340_QL65&keywords=quaternary+extinctions&dpPl=1&dpID=51NF6ATE7JL&ref=plSrch

(Sorry about the length of the links)

I have a copy of Greg Paul's The Princeton Field Guide to Dinosaurs (2010) and I like it quite a bit.. Reasonably up-to-date, lovely art, a diverse selection of dinosaurs... The only one of your criteria it doesn't meet is #4. It's a pretty bulky book.

I've recommended it before, but My Beloved Brontosaurus is structured around this very thought—what did you used to know, and what has changed since then. It's a very accessible read and I highly endorse it.

I'm not sure if it's the most comprehensive, but The Princeton Field Guide To Dinosaurs is really good.

25 Fossils (https://www.amazon.com/Story-Life-25-Fossils-Evolution/dp/0231171919/ref=sr_1_1?s=books&ie=UTF8&qid=1522703337&sr=1-1&keywords=25+fossils)

It's probably the most accessible, easy-to-understand paleo book geared towards adults that I've come across. I use it when I teach my upper-level undergrad students, and then I gave a copy to my non-science mother who loved it...so all spectrums covered.

Read this book, it's very easy to follow and very absorbing.
https://www.amazon.co.uk/Flying-Dinosaurs-Fearsome-Reptiles-Became/dp/0231171781/ref=sr_1_24?ie=UTF8&qid=1505919515&sr=8-24&keywords=dinosaur+birds

Prothero's "Bringing Fossils to life" was one of the into textbooks we used when I took an undergrad invertebrate paleontology class and it is a good introduction. The other book we used was exclusively an invertebrate paleo book, but this one has a decent amount of vertebrate stuff as the author himself researches fossil mammals and Cenozoic stratigraphy.

Worth noting, the title is likely a homage to this...

https://www.amazon.com/Dinosaurs-Darkness-Life-Past-Thomas/dp/0253337739

I don't know as much about online resources, but I've recently run into a book called The Complete Dinosaur. Far from being just superficial dinosaur trivia, it has a lot of scientific papers about the morphology, ecology, evolution, ontogeny, and history of dinosaurs.

This one's fiction - sort of Jurassic Park on 'roids.

https://www.amazon.com/gp/product/B07WC7FJ4B/ref=x_gr_w_glide_bb_sout?ie=UTF8&tag=x_gr_w_glide_bb_sout-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=B07WC7FJ4B&SubscriptionId=1MGPYB6YW3HWK55XCGG2

https://www.deviantart.com/jes86/art/AGE-OF-MONSTERS-809036276

(This is a good start.)[Encyclopedia of Dinosaurs and Prehistoric Life https://www.amazon.co.uk/dp/0751309559/ref=cm_sw_r_cp_apa_GI7QzbC3DZ15K] Darren Naish is good but I doubt much of his work will be in whatever language writes palæontology.