#1 isn't a "mistake" it's a preference, really. Also, I'm really not sure about putting the template files in the directory with the other files. Then I guess I'd have to add something to my build script to copy them to a hosted directory?
#3.1 IMO, Is actually more of a mistake. Imagine you have 3-4 modules, which one do you define that underscore service in? Oops, better make a 5th "common" module, I guess. Just to include something that you could have injected with $window. Notably, the underscore service is also missing that it should be injecting $window. How is he going to test that? Scrap the whole underscore service, and just inject $window where you need something from the global scope.
#9.1 Protractor - Protractor is great. But it's a little hefty for true "unit" tests. Jasmine with `angular-mocks` works a little better for unit testing Controllers and Services, where Protractor is better at testing directives and full end-to-end tests.
and one thing I'd add to this list:
#11 - Overly "DRY" Jasmine tests.
A lot of Angular developers I know are way too fond of drying up their Jasmine tests with nested describe() blocks and lots of beforeEach() clauses. Tests should really be "DAMP" not "DRY".