Thundra in this Marvel Animated Universe is evil. She was part of the Frightful Four on USM. That's where I was basing my idea off of.
Thundra is a dimensional-hopping queen of another dimension. She's probably aware Bruce has turned into the Hulk in other dimensions. In my scenario, Thundra sought out a fresh-out-of-college Bruce and got the relations she wanted (or if that's unacceptable, she just stole Bruce's genetic material), and had Lyra. Then when it was time for the gamma accident to create the Hulk, Thundra put a young Lyra within range so Lyra would get exposed, creating Thundra's desired warrior or so she thinks. But Thundra had to leave Lyra alone (after all, Thundra doesn't want to be exposed to gamma radiation too, it'll kill her). During the chaos of Bruce's first Hulkout, Thundra loses track of Lyra, but little does she know Lyra and Hulk have encountered each other, and Lyra's presence soothes the Hulk and Hulk takes Lyra away. Bruce is curious how Lyra survived the gamma radiation, so he does blood tests, and eventually finds out Lyra is his child. Years pass, Lyra becomes a worldly teenager, and she has a calming presence that has kept the Hulk from basically destroying everything in sight because the Hulk recognizes Lyra as his daughter too and he doesn't want to make Lyra sad or disappointed. Thundra, meanwhile, continues to search for Lyra, and Thundra is using the Frightful Four as a means to an end to get what she wants. [
Bruce and Jen don't have to be forty in this scenario (plus they age slower anyway), Rick is in his mid-twenties at the time of SMASH, and we have a different take on Lyra that makes Lyra more likable and human. It works out.