I guess I was lucky when I managed to successfully install AX 2012 R2 CU6 EP on SharePoint 2013... After this, we concluded that the first issue was solved (rememeber the missing method in class SRSReportHelper?) and a co worker went to a customer to do the install. Guess what? It failed with a new error (I'll update this post with the details later)!
After a lengthy support process with Microsoft trying all sorts of clever tricks (tweaks), we recieved a couple of hotfixes (both application and binaries) that finally solved the issue. I don't exactly know if it was a combination of the tweaking and one/all hotfixes, but my co worker finally managed to successfully install EP in two separate installations. And right now it seems that we are experiencing yet another issue (a little bit early to conclude).
The reason for sharing this, is to warn about going to customers without testing the installation on the exact same software combinations as on the customer side and that you are prepared to discover new issues. This burns a lot of time (impossible to estimate the number of hours required) and it does not make a good impression at the customer side (trust me - they expect that we are experts, but that's almost impossible with the current maturity of EP on SharePoint 2013). I regret to say this, but Microsoft must put more effort into this combination and provide much more information on TechNet on how to successfully install EP on SharePoint 2013. The current information is outdated and references needed KB articles (hotfixes) that in fact are included in CU6, but NOT DOCUMENTED IN the release notes for CU6!
I'm tempted to recommend choosing SharePoint 2010 if possible until Microsoft makes installing EP on SharePoint 2013 to a more enjoyable ride and maybe also update the site template to SharePoint 2013 (is still 2010). Field testing the compability with SharePoint 2013 is NOT the way to do this since both partner and customers are suffering big time.
All issues we have discovered are related to site creation (EP deploys fine without site creation during installation, but as soons as you try to create the site either after deploying EP or as part of the installation, it fails).
I will update this post or post a follow up when I have the details.
Follow up (November 5th 2013):
It seems Microsoft was lucky this time - no hotfixes was required and my collegue managed to get EP installed on SharePoint 2013 together with Microsoft support. We used AX 2012 R2 CU6 with binary build 6.2.1000.3198 released in September. I don't have further details about the magic configuration change done, but it seemed to be related to a combination of an SharePoint Update changing something around the requirements for the Claims Service. I have to look into the support incident to get to the details and right now, I'm too busy to dig into this.