The size of ob.el is quite manageable (between the size of 
org-list.el and that of org-table.el) and I think ob-eval.el 
and friends really belongs to the core Babel library.

As for handling "large" files, I use this:

#+BEGIN_SRC emacs-lisp
(defun org-cycle-global ()
  (interactive)
  (org-cycle t))

(defun org-cycle-local ()
  (interactive)
  (save-excursion
    (move-beginning-of-line nil)
    (org-cycle)))

(global-set-key (kbd "C-M-]") 'org-cycle-global)
(global-set-key (kbd "M-]") 'org-cycle-local)
#+END_SRC

I made a video to demonstrate it quickly:
https://vimeo.com/55570133

This helps me survive in files like org.el and org-agenda.el :)

On the overall, I really think this is an improvement.  Unless 
you find a bug in the dependencies and/or find a bug in the way
dependancies are handled, I'm in favor of committing it (modulo
some work that needs to be done to reorder/clean the section a
bit.)

Let me know,