It is true that there are often challenges when upgrading between releases of BusinessObjects but this has always been the case as it has been for all the other BI and software application vendors too.
A few rules of thumb for BusinessObjects software are:
1. Never upgrade to an x.0 release - always wait for at least the x.1 release and even the first or second service pack of that release
2. Never attempt to perform a release upgrade if you have not done one before. Get training and experience first or use a reputable BO Consulting company
3. Experiment with the new release on a sandbox environment to become familiar with the changes and find any major issues before attempting a migration to production
Once you are stable on a BusinessObjects release, it is worth staying there for a while.
Update April 2014 : BusinessObjects BI 4.1 has been out for 8 months now and is looking like a stable release. Expect to see a lot of activity moving to this release over the next year.
Update September 2014 : BI 4.1 is now at Service Pack 4 (SP4) which corrected multiple issues in earlier service packs (SP2 and SP3). As more customers move to BI 4.1. more experience is gained and the platform improves. Main features attracting customers to BI 4.1 are improvements in Web Intelligence, Mobile Dashboard support and support of Desktop Intelligence.
Update February 2015 : BI 4.1 is now at Service Pack 6 (SP6). Both SP5 and 6 have been stable. Most BI 4.0 customers are also migrating to BI 4.1 and many more XI 3.1 customers are also migrating since XI 3.1 goes into a maintenance only support mode ( no more service packs or fix packs) after Dec. 31, 2015. The next major release BI 4.2 is currently scheduled for end of the year.
Update December 2015 : BI 4.1 SP7 has just been released. BI 4.2 is in Customer User Validation phase and will not be released until 2016. The jury is still out regarding if the quality of software updates has improved but new QA processes have been implemented by the SAP BusinessObjects development and support teams this year.
Update May 2016 : BI 4.2 SP2 was released at the end of March. There are quite a few new features including to the Upgrade Management Tool (UMT) which is used for migrating content from previous releases. It is now possible to handle incremental updates and moving certain types of content instead of all. There is also a new mechanism that allows part of the update to be performed while the system is still running. There is also a new Recycle bin feature for public folders in case you accidently delete a report. Organizations still running BusinessObjects XI 3.1 are now looking to go straight to BI 4.2.
Update October 2016 : BI 4.2 SP03 is now the latest version released at end of August. It has a lot of new features for a service pack including additional new functionality for Web Intelligence like cascading prompts for input controls, references and further enhancements to the new discussions. The Administrators cockpit has also been further enhanced to provide more options. So far, stability looks good.
Update April 2017 : SP03 has proven to be a relatively stable service pack that many BO customers have updated to. The next service pack, SP04 is now in beta and scheduled to be released in May. Again, it promises to have a bunch of new functionality for Web Intelligence including full parity between the Java and dhtml clients, an optional new UI and many new graphics
Update September 2017 : SP04 has now been available since May and there were additional quite a few code changes . The first release release had multiple issues. Some were addressed in the two subsequent Fix Packs that have been released. The general feeling was that it was not as stable as SP03. However SP04 was the first version that included SQL Server 2016 support so many customers wanted to install it.
Update February 2018 : SP05 was released in December and there were further enhancements particularly to the new optional HTML5 Fiori portal that can now be used for consuming BO reports. This first version has some issues around installation/upgrade but too early to judge its overall stability yet.
Update July 2018 : Like all the previous BI 4.2 Service Packs, SP05 had multiple issues when first released and really did not completely stabilize until Fix Pack 200 (after Fix Pack 100). It is now at Fix Pack 400 and SP06 is in beta testing and should be released soon.