There is no issue in 2.52 / 3 in Unity 5. The obsolete API message is only visible because we exported the package here using Unity 4.6, you can download the same thing from unity asset store and you won't get the message there. There is no known issue updating, post the error you get and should be able to work it out from there.
Well, I tried a different way to update:
I first updated to TK2.5.3 in my Unity 5.0.1 (it works fine).
After that, I updated Unity to 5.0.2 and, when opening the project I get the message on image 1 (attached) about obsolete API.
If I click "No thanks" and continue loading the project, I get the error on image 2 on the console, about "LoadAssetAtPath".
I tried to choose the "Go ahead" option (automatic API updater) and it seems to work, but it changed several code and prefab files in TK2D, and I am not sure about what it actually did.
Note that Integrity Check is success after automatic API upgrade.