I definitely like having credit numbers as they save a lot of time in communication and reference. There have been some numbering issues, as mentioned above and I was hoping v4 would be used as an opportunity to fix those problems.
I would like to see consistency in numbering across all rating systems. For example, "Controllability of Systems - Lighting" is IEQc2.2 in EBOM and IEQc6.1 in NC. I think they both should be IEQc6.X. (The "X" can be different in different rating systems, but the "parent" number should be the same). This would help avoid miscommunication for LEED APs working in multiple rating system platforms.
I would also like to see consistent use of the "parent/child" numbering system. Many credits have a X.X numbering structure to indicate that the credits deal with a similar sustainability attribute. For example NC SSc4.X credits all deal with Alternative Transportation. EBOM EAc2.X credits all deal with Existing Building Commissioning. I like this system, but the EBOM MR credits stray from this structure inexplicably - MRc1, 2.1, 2.2, 3, 4, and 5 all start with "Sustainable Purchasing"... why not MRc1.1, 1.2, etc. Also MRc6,7,8, and 9 all start with "Solid Waste Management". Again, why not MRc2.X.