In general, I would say that 5th is the best edition I have enjoyed due to the rules design (and I have every edition still sitting on my shelves). But there are definitely a few critiques that go with it.
My first is the fluff vs crunch others have mentioned. Previous editon sourcebooks have on average always had more rules than what we see now. I like fiction, but when I buy a game book I want the game represented in it moreso than the fiction.
To give an example, here's a comparison between Unwired and Data Trails:
Unwired is 207 pages. 136 of those pages have mechanics and game content. Technomancers are fully detailed and still have all their now-missing goodies (like Paragons).
Data Trails is 183 pages. 74 of those pages have mechanics and game content.
The game content between these two books is also vastly different. Commlinks in Data Trails seem neglected. What is defined as the single greatest piece of gear to a runner gets some bland phone apps and the inability to run actual programs. Rules for Form Factor are light, almost negligible (add to cost/availability, but gain nothing like armor rating, etc like previous edition cases). The highlight of the book should be the section on modifying gear, but it too comes up light. Adding Persona Firmware sounds great, except there's no table for what the Persona's stats are (Persona stats are always linked to a device, so what device do you use?). I think the idea behind some of the new content is good, but I come away with the perception the writer knew what he was envisioning already and didn't think to write all of it out for the rest of us to comprehend (so we're left guessing how some stuff works).
Chrome Flesh. I don't need to say much here. Yes it has lots of fluff, but what's included in rules more than compensates. Its jam packed with old and new goodies. After Run Faster, it is by far my favorite sourcebook.
Looking back at some other sourcebooks, Street Grimoire and Run n Gun were good, but they could have been better. Here we come back to customization, which seems sorely lacking in 5th edition. Street Grimoire had none of the spell creation/modification of previous editions. The sections on item creation seemed a bit drab, not enough info on using refined, radicals and orichalcum. The Talismongering chapter went on and on, and then didn't really offer any crunch to make reading it worthwhile. Oh, and Spirit Mentors. Guess most of them from previous editions have been wiped out by Horrors, so we're left with fewer choices.
In Run n Gun, the big hole is definitely all the previous gun customization being gone. Instead, there's a chapter dedicated to the mathematical details of blowing up buildings. I don't mind the explosive creation part, but I'd say the rest is of rather limited usage to players compared to weapon tweaking.
Last thing I'd say is storylines. Universal Brotherhood was by far the best. Followed by love of that wacky Harlequin. Then all of the interesting characters from the classic modules and campaign books (Mercurial, Euphoria, Deus, various dragons, etc). Sadly the it-kills-your-characters nanovirus comes in last. Way too apocalyptic unless your goal was to bring a campaign to an end (and possibly put you on the hit list with your fellow players). We need adventures with more iconic NPCs and returning enemies you love to hate. The campaign books are nice if you want to fill in the blanks for your group, but sometimes its hard to beat a good old fashioned module.
The good thing to take away from all of this is that there's always room to add more to the game with future books. I'm hopeful that maybe there's a Big Book of Customizing out there on the horizon to bring back a big portion of mechanics that are missing. Or individual pdf supplements that will fill in the gaps. Either way, 5th edition is a good successor to the previous editions, and on the average I've been pleased by most of the current products.