Having used Pro/Intralink 3.3 and migrated that to Windchill 7 at one company, I have seen changes/improvements along the way. I have also been at a company that went from Pro/PDM to PDMLink7 with no outside help. I did an upgrade from PDMLink 9.0mo50 to 9.1m060 yesterday. It took all day, but is up and running.
Migration will always be an issue. The changes we had to implement to the Pro/Program portion of our files to change parameters from Intralink to PDMLink meant that we had to export all files, run a batch ModelCheck program and then do an automated import into PDMLink. No direct migration tools from Intralink DB to PDMLink DB. If you plan on using the parameters provided by Windchill, you cannot do a direct import. The files must be massaged first or you will never get them updated. We also had to develop new formats to incorporate the proper parameters. The site that did Pro/PDM to PDMLink did it all manually with no customization for the parameters being used in the drawings. My current site also does not use the parameters efficiently in the drawings.
Windchill is Windchill. It is what it is and it is nothing but a giant toolkit for developers to implement an application on top of a framework. PDMLink, MPMLink, PartsLink, ProjectLink, PDM Essentials and Intralink (since 😎 are all built on the same core Windchill technology. How much would you expect to see in differences when they have the same core? Some pieces turned on, others turned off is about the extent of the customizations that tailor each product.
One thing that was mentioned was setup AFTER the system was installed. Is your implementation of Pro/Intralink 3.x so long ago that you forgot that OOTB it had no roles, folders, groups, lifecycle states or revision rules. These all had to be defined and setup by the company system admin. The Windchill products are no different. How much can you expect PTC to put into a 'canned' solution without knowing what your company wants to do with its product. I agree that there may be more that could be done, but the end user admin still needs to add users and assign them to groups for the roles. Essentials should be easier since you only have 1 small group of users to populate the system with. I have had 400 users in my Windchill Aphelion system.
Training is still required and is not an expense item. Training is an investment for you and your company. You needed training to set up Pro/Intralink 3.x, you need training to setup PDMLink or Essentials.
Hardware is 'cheap'. While most companies did not have a second mirrored Pro/Intralink system, it was recommended for testing upgrades, patches and customizations. Windchill is no different. You still need 2 servers, application and database. In my current setup, I am working on a migration to 10.0. That requires all new hardware since I must be running on a 64-bit OS. I am also in a secured environment, data and computers go in, nothing comes out. I have 4 32-bit servers and 4 64-bit servers to support my current and future requirements. I also have 7 virtual servers for initial testing on my unclassified network. Practice for an upgrade is essential. Even with what I had practiced and documented, I still had some minor glitches yesterday. I know what to do to resolve them, but they still cause a mild heart attack when they happen.
Enough rambling, take it all with a grain of salt. Each implementation is unique and there will never be a 'one size fits all' OOTB implementation.