Split SSIS project in to multiple files to avoid merge hell
I've been using subpackages successfully on multiple projects. The typical scope is one sub-package per target table.  I also have a few utility packages eg Disable Indexes, Rebuild Indexes (on a table, passed as a parameter). A single "Master Control Package" is mostly Execute Package tasks.

With the Project Deployment method, devs need to be aware that prematurely checking in their changes to a single package can block the deploy (it wont deploy a project until all the packages validate cleanly).