During a site upgrade of Open Cart from version 4 to version 6 I ran into some problems. There were of course the normal issues going between two major versions, but I was finally able to overcome those by upgrading first to version 1.4, then to 2.0.
However, I ran into two unexpected issues after successfully reaching version 6. The first: I was trying to install the pavilion theme and kept running into odd errors. I was able to resolve these by upgrading to the latest version of the pavilion theme, apparently pavilion does not have its supported version numbers quite up-to-date yet.
Note: in the settings table is a new category type column called code I believe. This new column needs to be updated with the values from the old column, none of the upgrade scripts do this.