I love these when they actually fix something of mine, but that's rare for the most part. The main problem I have with them is that they mess up GRUB, and they mess up my NVIDIA drivers.
GRUB messes up because Ubuntu just sets everything to the default menu, which is Ubuntu, safe mode and memtest. I never use safe mode or memtest, so I usually get rid of those. I also have an XP partition which I would like to see in the GRUB menu, but it doesn't like to put that in either. This stuff isn't a huge deal, it's just a matter of changing the configuration file. Unfortunately from a less-technical perspective, a user has just lost access to their Windows drive and has no idea how to fix it. Not a good thing! I showed my girlfriend how to manually edit her grub/menu.lst file to put Windows back, but unfortunately sometimes she forgets how to do it correctly and fudges the whole thing. There goes the whole computer! Ubuntu: FIX THIS. You may hate Windows, but that doesn't mean the people who use your system hate it too.
Now the big part that pissed me off the most. I got a brand spanking new GeForce 8800 in December which runs beautifully. Unfortunately, the open-source NVIDIA drivers don't work very well for it. I can run at 640x480. Now, I'm not really a wizard with X, so when it comes to touch the xorg.conf file, I'm somewhat scared. I don't want to make things worse, which is usually what happens when I touch Linux's private parts (anything not in my home folder). So what I do is just download the wonderful little installer from NVIDIA's website and get that going, which for the most part fixes the problem. While this is good, it would be nice if you could run it from X and just have it complete its install on a boot-up script or something, having to CTRL+ALT+F1 and shut down X is not something the average user would like - or know how - to do. Anyway, I just wish that the kernel update would also keep my NVIDIA drivers intact.
EDIT: Apparently it wasn't just the video card drivers that the update messed up, looks like my printer is dead too. Fortunately I have an XP install that WORKS.