I think it depends on what you hope to do during the two weeks.
If your priorities are WDW and Universal, then Deb's split is an excellent suggestion as staying on-site does give you excellent perks at both resorts (transportation and early entry at WDW and Front of line at USF/IOA). The WDW transport option is a big bonus if you prefer not to have a rental car, and the Universal resorts are within walking distance of USF and IOA.
If you plan on spending quite a bit of time outside of the main parks ( maybe visiting SeaWorld, the water parks, shopping, Kennedy Space Centre, etc., etc.) and will have your own transport, then staying on-site becomes more of a luxury with perks you might not use to full advantage.
There are some great hotels all around Orlando, but the Disney and Universal ones take some beating as resorts in their own right!