A question that I have seen reoccurring across our social networking feeds is will my existing Cydia tweaks be compatible with iOS 6.1 and the iPhone 5. Unfortunately this is a pretty vague question as every Cydia tweak has its own dependencies and developers who may or may not be actively working their tweaks. For the most part however, I can confirm that most, if not all of the popular Cydia tweaks have already been updated for iOS 6.0.x. You have to realize that tweak developers have had a long time to test out their tweaks on A4 devices tethered to bring compatibility and some of them probably had early access to the A5 developer iOS 6.0.x Jailbreak.
It wouldn’t make sense for developers not to update their tweaks, as they actually make quite a bit of money off tweak sales. The biggest time for developers to make money in the Jailbreaking scene is right after a Jailbreak is released, so you can be assured it is at their top priority to ensure compatibility.
What about the iPhone 5 you ask? Well, again the answer to the previous question could more-or-less apply to the iPhone 5, but Saurik(The creatoer of Cydia) recently answered the question on a Reddit Q&A thread that goes into better detail…
"Usually new firmware causes more serious problems than new hardware; in the case of a slightly-taller-but-still-largely-the-same-thing screen, most packages in Cydia don’t really have normal “app” UIs: they are extensions that modify functionality of other things, and so aren’t affected. The main things that come to mind are things like biteSMS, WinterBoard, iFile, and Cydia itself, all of which are trivial modifications to take up the new vertical height (in fact, for at least WinterBoard, iFile, and Cydia, I believe it is just “throw a new Default.png in the folder and you’re good to go”, as they all do programmatic layout)."
So, there you have it. There will of course be some tweaks that will not be compatible with iOS 6.1 and the iPhone 5, but the numbers should be actually lower than in past cases this time around. The owner of BigBoss did chime in today on Twitter however, that the tweaks that will likely need the most updating for the iPhone 5 are “home screen, lock screen and switcher tweaks, and perhaps a selection of themes.”
As I said previously however, the turn around time on these updates should be pretty quick and you should only really encounter troubles with lesser-known tweaks than popular ones. Hopefully that answers a majority of your compatibility questions.