I had this too when I restored from a jailbroken iPad 3 to a stock iPad mini... and I kinda liked it!
The only annoying things were (A) no way to customize it and (B) I would often miss the "x" dismissal button on a notification below it, and inadvertently open a Yahoo! weather web page in Safari.
Anyway, with today's release of the "evasi0n" jailbreak, I updated to iOS 6.1 and ran the jailbreak on my iPad mini. Now I see the Weather widget is gone. And, I now have the Weather app on my springboard (which works fine, albeit as an iPhone app, in 1x/2x mode) -- right next to Cydia.
So, is there any way to bring the weather back to my notification center? I'm guessing now that I'm jailbroken there will be a more straightforward way? (Or will I have to involve LockInfo or Intelliscreen X?)