As mentioned earlier, you may approach a portfolio template project from the content authoring side of the shop first (and some schools DO start by creating matrices and wizards for program evaluation purposes only later to consider using the personal publishing features that the portfolio tool affords) or you can begin the project with the goal of creating a very specific portfolio output. Whichever way you approach a project like this, you will quickly realize that the template you create may depend on very specific wizards, matrices and/or forms to describe "valid" portfolio content.
Once students have begun to create valid content (and portfolios from it), making changes to form schema or wizard and matrix structures may become difficult (if not impossible) to do. You should consider how your team will "roll out" new versions of the portfolio system to your users, particularly if you plan for your users to be building their portfolios over extended over multiple semesters or even years.
Since each viewing of a student portfolio essentially reassembles all of the content and transforms it, changes to the underlying template will change portfolios that students have already created using that template. For that reason, radical changes to templates in use are not recommended.