Alright... now here is my idea of how Mew and Mewtwo could get together.
It would be after Mewtwo's Return. Mew would eventually get sick of remaining alone and would remember the time she spent with Lucario and wonder if it would be possible to make a new body for him... but before doing so, she would head to Mewtwo's place to play a prank on him, as she would usually do after Mewtwo's Return.
Since she is intent on pairing up with Lucario after reviving him, she decided that her final prank on Mewtwo should be a big one... but the prank doesn't go as planned as unstead of causing hilarity, it unstead causes Mewtwo to lose patience. That final prank was aimed at his feelings, seeking to make fun of how he supressed his own feelings by making them surface against his will.
Mew, intrigued by Mewtwo's reaction, would be overcame by her curiosity. So... the male kitty has a heart, after all...
The two would begin to learn about each others, learning of their differences... and although he denies it at first, Mewtwo is amused by Mew's playful nature. Mew, her, would have her curiosity bring her back to him time and time again. The first hints of a relationship begin to appear...
Mewtwo's curiosity will eventually emerge, causing him to experiment on Mew and find out about how his DNA is different from Mew's. He would also learn to appreciate Mew more and more, her different point of view allowing to see things he would have never seen before. He would also find out that behind her innocense and childish attitude, Mew has a surprisingly deep and optimistic way of seeing life, having love and care toward all creatures. Mew, too, would benefit from being with Mewtwo, learning about stuff she would have never paid attention to before and also learning that there was beauty in technology as well. Furthermore, their powers would complete each others, Mew's positive powers bringing a balance to Mewtwo's destructive powers.
But what will cause Mew to actually go to the next level is when she will realize that while she has been seeking for a being who genuinely cared for her, she had ignored the one who had stood for all his life in front of her, caring for her as an actual being and not just as the Legendary Pokemon of Light and Purity. Mewtwo would also realize that if Mew did not care for him, she would have never paid this much attention to him... and slowly, the friendship would mature into love.
There it is, how I see Mew and Mewtwo getting together.