After the fall of the Installer App, Cydia became the go-to standard for jailbreaking apps on the iPhone. As such, the APT repositories and the entire backbone of the jailbreaking community is based on the house that Cydia built. Everything from the developer kit to the software used by the jailbreak community starts in Cydia, therefore, you get native support while working under Cydia that may occasionally bother you in Icy.
Reliable Repositories and Software
This may be a personal issue with Icy, but I’ve yet to install it successfully on my phone. While I have messed around with the interface on other iPhones, the actual program seems to refuse to install itself on my phone. While this may bias me towards Cydia, I still see it as a more reliable engine, add to that the fact that Cydia comes pre-installed with more repositories, it’s a clear winner in this category.
Support from the Community
Because Icy is a relatively new development in the jailbreak community, Cydia has many guides available on how to get apps working through it. Icy on the other hand can leave you with your hands up in the air trying to troubleshoot a problem that has little to no documentation.