To me it seems mostly that SK wants out of the UE3 deal, maybe get their money back or something and that the improvments they have been making not to be categorized as an update of UE3 but rather is a new engine all together and do not have to pay licenses to Epic because of that...
Actually they're suing for more than 75,000,000 USD. At least that's the jurisdictional amount mentioned in the pdf.
Another thing SK claims is that Epic didn't allocate enough of its human resources to the engine development team but rather chose to develop their own games. This is going to be very hard to proof IMO.
Also they're claiming that parts of that "game code" was actually "engine" code, which wasn't made available to devs. Their claim is that such behaviour runs contrary to the spirit of the licensing agreement. This is going to very hard to prove as well.
Now as for Epic slipping the release date of the final version twice (Xbox360, PS3), SK might have a case here.