I would say your findings point to one thing here: Your formula is working out what div is the hardest to win (based on how good the top teams are), however I would define the "Toughest league" as one that is tough just to stay in it.
That's kinda what I went for in my first post to determine "toughest league". Here's the total list of just adding up the CR of all the teams (+500 per bot):
league rank
III.16 - 3240
III.14 - 3258
III.3 - 3267
III.12 - 3605
III.6 - 3649
III.7 - 3684
III.5 - 3755
III.10 - 3764
III.1 - 3819
III.9 - 3860
III.13 - 3906
III.15 - 3943
III.4 - 4092
III.11 - 4094
III.2 - 4175
III.8 - 6544
III.10 comes out a lot better here, and III.8 looks like the big wimp. I suppose you can look at this list as "the hardest league to avoid relegation in" ranking. A rough calculation compared to Simon's fine tuned formula, but some more fuel for debating.
tripsatx - sorry to jinx you with the shoutout
One thing known to factor very high in the CR is cup performance, and your team has had deep runs the last two seasons.