Bailey allowed a ton fewer hits (5.86 per 9 innings compared to 9 per 9 innings for Cueto), a ton fewer HR (0.46/9 compared to 0.81/9) and had a lower WHIP. Cueto ran with the much better walk rate and a slightly better strikeout rate.
Personally the biggest things each guy has over the other is Baileys ridiculously lower hit rate and Cuetos much better walk rate. I like the guy allowing more than 3 fewer hits per game myself.....
IMO, the reason for Bailey's 3 point lower hit rate was nothing more than luck. He had a .254BABIP in Louisville. You could maybe argue that pitchers can control this stat somewhat against minor league hitters, but Bailey's career BABIP was .309 before he reached Lousville. Chris Welsh might call this being crafty, but it seems more realistic to attribute this to good fortune and the fact that Chris Dickerson can cover half the field with a broken leg. Here's both their numbers in the minor leagues...
Bailey: 317.2IP 3.43FIP 3.43ERA .297BABIP 9.85K/9 7.15H/9 4.23BB/9 0.51HR/9
Cueto: 348.1IP 3.05FIP 3.28ERA .301BABIP 9.26K/9 7.76H/9 2.12BB/9 .062HR/9
Bailey's stuff is obviously a tick better, but Cueto has out pitched him in my mind.