A true anime shipper isn't stopped by trivial details like two characters not living in the same universe. Sure, cross-series anime ships may consist of characters who never actually meet each other, but that doesn't mean they aren't a great match or that fans can't enjoy thinking about them together. After all, fan fiction has spliced Twilight with Supernatural for years now, so why can't anime fans do the same?
Everyone has their own preferences when it comes to ideal relationship dynamics. Some of these fantasy anime ships are wholesome and mutually fulfilling, like Phichit Chulanont of Yuri!!! on ICE and Shoyo Hinata of Haikyuu!!. Others are delightfully disturbing, like the imagined liaison between Akira Midousuji of Yowamushi Pedal and Sawa Nakamura of Flowers of Evil. Some, like Faye Valentine of Cowboy Bebop and Motoko Kusanagi of Ghost in the Shell are totally badass power couples.
Hopefully, at least one of these crossover pairings will get you inspired to come up with a few of your own.
Few people want to break up Bulma and Vegeta, but should the Saiyan prince and his mad scientist wife ever stop getting along, Vegeta will want something pretty specific from his next relationship. Citing his Saiyan blood as the reason, Vegeta makes it pretty clear he prefers strong women. As a human, Bulma may not be able to match his physical strength, but she never hesitates to put him in his place.
Another woman who fits this criteria is Olivier Mira Armstrong, a commanding officer in the Amestrian army. She may not be able to defeat him in battle – even the best swordplay encounters some difficulty when put up against a Super Saiyan – but she could easily command his respect and esteem with the sheer force of her personality. Meanwhile, Olivier would dig Vegeta's pride and his relentless drive toward self-improvement.
Tohru Honda spends years of her life embroiled in the Sohma family's dismal affairs, and while she obviously adores them, the emotional labor she constantly performs for them must be exhausting. That's why she needs a relationship with someone just as focused on the needs of others as she is. Ryuuichi Kashima might just be her perfect match.
Like Tohru, Ryuuichi is a total sweetheart, fully dedicated to his own caretaking duties. He has a preschool aged brother named Kotaro for whom he acts as a surrogate parent, and he works in a daycare center. He goes out of his way to help anyone with their problems. Also like Tohru, he has a tendency to ignore his own needs and work so hard he literally makes himself sick.
Since both Tohru and Ryuuichi are so in-tune with the needs of others, they're both best suited to people on the same wavelength. Tohru might not notice when she needs a break, but she'll notice when Ryuuichi does and make him take one – and he'll do the same for her.
Motoko Kusanagi and Faye Valentine, both utterly badass women from action-packed anime series, make perfect choices for an anime power couple. Faye works as a bounty hunter who plays an integral part of the Bebop crew, while cyborg Motoko Kusanagi serves as a major in the Public Security Section 9. They're independent, intelligent, women capable of holding their own in a fight. However, both of them spend most of their time working with men, and each is sorely in need of the company of a woman as awesome as herself.
Violet Evergarden and Decim both lack a fundamental understanding of human nature. For Violet, this stems from a combination of inborn personality traits and traumatic experiences as a soldier. For Decim, it's because he's not human: he's a living mannequin tasked with determining whether human souls should be reincarnated or destroyed.
Both Decim and Violet spend their respective series trying to understand human emotions from the outside, while struggling to understand their own unique experiences with these feelings as they start to experience them. Because the two of them share the same struggle, it would be quite touching to see them approach the problem as a team, and to experience romantic love with one of the few individuals either could successfully relate to.