I was a long time Ubuntu user up until 11.04. I ******* hate unity and refuse to use it.
What do you mean that some files are in the wrong place? What utilities are different? What do you mean by different? If you are comparing them to windows, OF COURSE THEY ARE DIFFERENT. GNU/Linux strives for POSIX compatibility!
Also, a note on flash in Linux. Adobe stopped updating flash after 11.2. They continue to offer security updates but there will be no new versions. It is being replaced by the pepper API; the only browser that implements this is google chrome.
Getting to the point...
Ubuntu Pros...
It has an easy to use install feature that can preform full drive (or partition) encryption WITHOUT requiring a special boot loader. This can be good or bad.
It is built on top of debian. This gives it access to most deb packages. Most software for linux is stored in deb files, so you get the max amount of free software available.
It's built on top of debian AND it can use debian repos AND it's own repos (such as PPAs). This makes installation of new software relatively easy since dependices are satisfied if you use apt-get
It's built on top of debian, so you get apt-get. apt-get ******* rocks. It's probably the BEST package manager add on. It will download and install programs AND their dependices for you. Linux distos like gentoo don't have something to do this for you. It works so well that slackware created it's own version to work under their system.
Ubuntu is basically made for newbies. It has an applet that will pop up when you install new hardware that uses proprietary drivers that will DOWNLOAD, COMPILE, and INSTALL your new kernel modules for you! Have you ever had to compile anything that involves thousands of lines of code? It takes ******* forever, and you have to fix the errors yourself. When I compiled wine on my Linux Mint Debian Edition it took over 2 hours, and I have an 8 core FX-8150 and 8 GB of Ram.
WINE (google it) has a PPA for newer versions of Ubuntu. This means you can get stock installations of WINE without having to compile them (and if you don't need special features then you SHOULDN'T compile software).
It's based on debian, so hardware recognition is really high.
Enough Pros, now some cons...
Unity ******* sucks (IMO). Gnome 3 sucks (IMO). KDE sucks. (IMO).
It's not true debian. The people on the ubuntuforums typically do a great job, but I've found with experience that they aren't as technically minded as the people that run debian.
Many people will assume you don't know **** about linux because you run Ubuntu. Before I stopped going to my Linux User Group, I found out that every person used ubuntu. They could not help me with basic issues and told me to go to the forums. You'll find that many people that run Ubuntu stay shy of the command line interface, and RELY on GUI tools to do everything for them. Ubuntu is so noob friendly that they have a tool to mount your partitions for you (instead of just copying and pasting ONE line in /etc/fstab and creating a directory).
It's not on a rolling release cycle. New versions come out every 6 months. This is both good and bad. Personally I like rolling releases, my system is always the newest version as long as I update. I never have to reinstall my operating system as long as they are supporting it. Do you really want to erase everything on your hard drive every 6 months (or 3-5 years till the support ends)?
I've just told you the tip of the iceburg. See this post for more info.... http://ubuntuforums.org/showthread.php?p=11619831#post11619831