This is a thorough spreadsheet. I'm author of the Custom Content Type Manager plugin, and your initial evaluation of my plugin has substantial errors. Here are my clarifications with numbers corresponding to rows of your spreadsheet.

9. Github? Seems a strange metric when WP uses SVN. Contributors and bug reports are welcome in my bug tracker.
17. What do you mean by "Override Post Types"? You can attach custom fields to existing post-types.
19. What do you mean by "Custom Tables"? Custom Database tables? Then no, the CCTM by design does not add those.
20. Custom Options/Settings pages: Yes, I've got a GUI page to control global as well as all local settings for every post-type or field created as well as hooks so developers can add their own options pages.
23. Custom fields for taxonomies: Yes, but indirectly: you can supply a SQL statement to a dropdown or to a multiselect field.
24. Custom fields for media: yes, from a very early version.
25. Custom fields for users: yes, added months ago in version 0.9.5.6.
26. Custom field for comments: Yes, but indirectly: you can supply a SQL statement to a dropdown or to a multiselect field.
30. Number fields: Yes. Note that the CCTM lets you add text fields and then you can apply flexible validation logic to that field, including number validation.
38. Flexible Relationships: yes, the CCTM is very flexible with this. The included GetPostsQuery class and associated UI is one of the best selling points of the plugin (according to user feedback).
39. Gallery: Yes. In the CCTM you add multiple images, movies, posts, etc. and then the "Gallery" is a formatting effect. There is an output filter to streamline this for users.
43. Custom Field Types: yes, developers can create their own field types: http://code.google.com/p/wordpress-custom-content-type-manager/wiki/CustomCustomFields
49. Shortcode: yes, there are several shortcodes supplied by the CCTM, including the powerful summarize-posts shortcode: http://code.google.com/p/wordpress-custom-content-type-manager/wiki/summarize_posts_shortcode
57. Full meta cap: yes, added 0.9.6.6
58. Unified theming: yes, this has always been part of the CCTM since inception. It's MVC architecture. Several functions are offered for use in themes: http://code.google.com/p/wordpress-custom-content-type-manager/wiki/TemplateFunctions
59. Templates/Views: Yes, this again was included in very early versions of the CCTM. It generates dynamic sample templates for designers.
60. Custom Management UI: Yes
61. Caching: Yes, persistent data is cached.
63. Import/Export: Yes, you can export/import definitions between sites.
67. Multisite compatible: Yes
68. Network-wide content types and fields: Yes
69. Network-wide content: Yes.

I'd appreciate it if you could update your spreadsheet: I don't want misinformation out there about my work.