It would appear that you have been bitten by a "bug" in the installer code--the error message is misleading according to the following report.
See if this thread helps: FMS 13 won't install on Windows Server 2008 R2. Complains that ARR cannot be found.
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip
I'd forgotten that FM13 Server (or its installer - not sure which) didn't like ARR 3.0 (maybe only in conjunction with Win Server 2008 R2, which is what I have - again, not sure), and so a manual pre-install of ARR 2.5 was necessary prior to installing FM13 Server. So much for the past. But now this update installer for 13.0v2 wants to uninstall ARR 2.5 and install ARR 3.0. So does that mean, by implication, that Win Server 2008 R2 is no longer supported by FM13 Server, or does it mean that FM13 Server now works properly with ARR 3.0 in all OS environments? Except that the latter would seem not to be true, since the installer is aborting in my OS environment.
Ok, so I called support, and for my situation I was advised to not use the update installer, but to use the full installer (184.108.40.2065) instead. I was told to uninstall FM Server and then to reinstall it. I was also told that if the reinstall didn't work, it would probably be because of certain IIS-related components, which I should manually uninstall, and then try the FM Server install again (this part didn't turn out to be necessary for me, by the way). When I did the reinstall, it got to the point where it said "Installing Application Request Routing 3.0..." and after several minutes passed, it came up and said something to the effect that it couldn't access ARR 3.0 via the internet, and that I would either have to enable internet access and try the install again, or manually install ARR 3.0 and try the install again. My server is firewalled off from the internet and it wouldn't be easy to open up access to the internet. So I found the web page (http://blogs.technet.com/b/erezs_iis_blog/archive/2013/11/27/installing-arr-manually-without-webpi.aspx) that explains how to manually install ARR 3,0, I reran the install again, and all was finally well. Of course, the uninstall / reinstall sequence meant that I had to upload my previously backed-up copies of my databases to FM Server, after the reinstall, and I had to reconfigure my schedule for the backup, but outside of that, for me at least, there was nothing else I needed to do.
My strong suspicion is that the update installer that I first tried to use was simply dying off without issuing a meaninful error message, i.e. to the effect that it could not access ARR 3.0 via the internet, and that I probably could have manually pre-installed ARR 3.0 at that point, and then used the update installer (again) to install FM Server, without having to go through a uninstall / reinstall sequence. But oh well...