eComic prices are completely artificial - bounded by Apple and the US Retailers.
The lowest ComiXology can physically charge is $0.99 US as that is the lowest price supported by Apple's payment API. Retailer backlash (the Direct Market accounts for approximately 90% of their sales) has forced publishers to match print prices for new release comics, putting new books at $2.99 or $3.99.
ComiXology started charging $0.99 for back issues, but Robert Kirkman (creator of Walking Dead) wanted to price his books at $1.99 and when he did, sales rose. Naturally, other publishers followed suit, making $1.99 the standard back issue price. The other factor is that by pricing books at $1.99, publishers can have sales where they drop them to $0.99. If individual issues were already $0.99, the only lower price the system could support would be free. It's messy.