I would start off by saying, the new applications are great and highly usable. Many thanks to the Populi team for all the hard work that went into developing it!
One thing that makes our student application experience a little difficult is that the application page is very long. It can get pretty confusing if you have to refer back to a section or come back to the application later.
My suggestion is to make the application a multi-page form based on categories such as: personal information, academic history, program information, etc. The form header could have a horizontal line with links to navigate to the various categories in the form.
One example of this type of form can be seen in Machform. We use this form software for our website's contact forms. They have a video showing how their multi-form forms work: http://www.youtube.com/watch?v=Gs2q9JnMnWs - just watch at the end to see how the form appears.
I believe this would make the form filling process seem less overwhelming and more organized.
Thanks,
Daniel