In my experience, there can be some advantages to doing the upgrade as a migration as opposed to using PUP updates.
First, if there are any schema changes in a new version, there can be some issues when doing the PUP updates, which will have to move the data, attempt to change the schema, then re-import the data if a table change is made. If importing the Org Key and Backup during a migration, since the server is effectively new and empty to start, it will already have the adjusted schema, and only needs to import the data from the respective tables.
Second, I like the flexibility that a migration offers (particularly in a virtual environment). If for any reason your migration fails, you can simply bring the old servers back online while working on a solution, or attempting to migrate again. It works on hardware as well, but then you would be occupying multiple physical boxes per server.
Lastly, since you are on a version prior to 3.3.0, you would need to apply two PUP updates to get to current version. You could migrate directly to the current verson (3.3.2 mp2).
The main questions I would have for you are:
Is it a single server, or a cluster?
What features are in use (i.e. Web Messenger, Email Encryption, Whole Disk Encryption, NetShare)?
Is it on hardware, or VMware?