Honestly I'd be ok with it if the creators got more money from the digital issues. If they aren't then they should definitely be cheaper.
What I know is this:
At every comics shop I have regularly frequented in the past, if I have a decent sized pull list (10-15 titles a month), the owner will give me at decent discount on new books. Typically 15-20%. Sometimes higher. This would mean paying $3.20-3.40 for a book with a $4 cover price.
If I was to buy my books on DCBS, I would get 40% off regular cover price (not counting a flat shipping fee). This would mean paying $2.40 for a book with a cover price of $4.
All of these retailers need to make enough money to stay in business. If they are giving me 15-40% off, their margin is a lot bigger than that. Furthermore, Diamond doesn't distribute books for free, so add their cut in.
Once they have given the retailer and Diamond their cut, Marvel/DC/Image/Whoever also have to pay to get the book printed. I am sure the big 2 are getting a good deal on printing considering they are ordering over a million books a month each, but the cost isn't negligible.
After paying all of those cuts and fees, what are Marvel and DC left with? Maybe 30-35% of cover price? Potentially less than that?
There is no reason why digital copies couldn't be $1.99 each on DAY 1, other than the fact that it would potentially hurt the specialty shops. Publishers would be making the same amount of revenue (or more) per book (assuming a 30% cut from Comixology), and I am sure digital sales would increase dramatically. For old back issues where the cost of producing the comic (paying writers, artists, letterers, editors, etc) has already been covered, issues should be 99 cents. Not as part of some limited selection daily sale, but permanently.