The cons:
No OpenGL support outside of dom0. You can still watch videos, but that's about it. I do a little webgl coding now and again, so I got around this by installing firefox directly into dom0.
I've had some issues suspending to ram, when I suspend while plugged in, and resume while on battery power or vice versa. It'll sometimes take up to 5 minutes to resume, or never resume at all. It'll also sometimes hang on booting a couple times after not waking from a suspend. I've never tried hibernating.
Copying and pasting between vm's is kind of a pain. Each vm has its own clipboard, and you use a special keystroke to copy from one vm's clipboard to another. Which means four keystrokes to copy and paste.
It uses a lot of ram. My laptop has 8G and it can handle running 5 or 6 vm's pretty well (Normally you need at least 3, network, firewall, and user os) but if I'm running something with a lot of memory usage, it can't run low pretty quickly. I use an OS specifically for passwords which has no direct network connection. Also unless you want to combine the network os with it, you need a seperate os for handling usb devices.
Backup kind of sucks. It basically creates a tarball per os. I have some special scripts to use borgbackup to overcome this.
Drive partitions kind of suck as well. Before you can use a drive partition, you have to attach it to an os. Then, you can decrypt and mount it. And then, when your finished with, say, an external drive, you must umount it, unmap it, and detach. If you forget to detach before you unplug it, and you try and use another external drive, the system will won't let you reattach it.
The pros:
Each guest vm has a template vm that has all the software. This makes dealing with many different vm's a lot easier than if they were all separate. It saves a ton in disk space as well. I have 24 vm's and use only around 90 Gigabytes.
Having the ability to separate clipboard, keystrokes, files, etc. between different applications makes me feel much more secure. The standard linux setup where all applications running under one user are completely trusted to read/write each other's information is just crazy to me. I do a lot of development, and there are so many build procedures which entail downloading random stuff off the internet to link and build into code being run. I find this horribly insecure. (I did try running two X servers once as two different users, but for some reason the graphics driver couldn't deal with switching between them, besides which, qubes is much more convenient in this respect.)
Having the ability to keep an os offline is a very nice thing to have for managing passwords and other important data.
Networking between the vm's works great.
os updates are simple, can be done from the command line and the gui, which, btw, is pretty sophisticated.
Copying files between vm's is easy and well thought out.
Creating and deleting vm's is very easy as well.
For what it does, in general, the gui is designed very well.
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Overall, I can live with the bugs, and am excited about the future of this project. It's helped me out a great deal with security (as far as I can tell, but who can really say anything absolute about security nowadays?), and does what it claims to do.
BTW, you'll have to accept running either Debian or Fedora on the guest vms to get all the disk space saving features. Although it can run any OS using a full virtualization mode, (including windows) I've only used paravirtualizations vms.
there's a borg community repo somewhere, if you want to share your qubes-scripts or a guide.