Isn't that a bit of a broader topic than what would be covered in these forums? There are several other PLM softwares outside of Windchill.
As for the comparison between the various systems, the ultimate method would be to use each one yourself for similar issues/processes and see how each one works compared to the others, breaking down their functionality in terms of speed/ease of use, ease of modification etc. to get a proper view of where each one's strengths and weaknesses are. Failing that, you would have to find people who have used multiple systems and get them to give a similar breakdown. I personally have only used Windchill PDM-Link and a quickly slapped-together Infopath form system for PLM and I don't know of any tables online that give comparisons between the various programs, so unfortunately I myself won't be able to help you out much on that one.
Engineering Systems Analyst
It also depends on what you are using the product for - drafting, xml documents, manuals, BOM, etc. You can find several studies comparing products based on the end use. Try searching google. And I always find gartner to be useful.
this company has specialized themself in business system evaluation (ERP; CRM; PLM).
For PLM they have over 2000 criteria they look at. They do not sale software and are very impartial in their methodology.
They also take into account if you have legacy system in place.
For instance, you have PDMLink 6 with no maintained licences. should you move to PDMLink 10 but or to Teamcentre with cheaper licences (not sure if this is true).
They have developed methotology over a decade which includes functionalities, consultancy required, data migration, training cost, licence cost etc....
Best of luck with your PhD