I have two MCs for the MG Sci-Fi TDW 1429.3; a male "Mon" and a female "Jo" (Josephine). Both will turn thirteen around the time the book starts. One of my biggest challenges right now is making the characters stand out for the reader, your thoughts are welcome.

Both characters are the youngest of a five person sports team. The female fences and the male swims, but both can do the other four sports in the competitions, at least to some degree. Mon is a lousy fencer.

Jo is defined; she has a vision impairment that requires the use of glasses that can record and focus. She is adopted, though none of the other characters know until the beginning of book 3. Of course, that her dad is a huge man and her mom is tall, shapely and blond while Jo is short for her age and has blueish skin should be a clue. Jo knows she's loved but her burning question is "why me?" Why was she adopted; she's different but why was she lovingly special? She's an Emo without the self-destructive behaviors.

Mon is the near mid child of nine. His special talent is staying in trouble most of the time. Nothing big, but if there's an accidentally broken window somewhere, Mon is probably close by. He has orangey-plum hair, usually fills the role of side-kick, and has a pinky promise with Jo to treat her like a sister. He started book 2 with a fascination for Miss Jones, a much older investigator type person.

At the end of Book 2 Jo and Mon came face to face with their "like" for each other. Jo piloted the star ship and Mon swam into a dangerous place to save the day. In Book 3 they will be the main characters.

Here's a scene from Book 1:

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Wilbur reached out, but his hand fell short. He pulled it back. “Look, we’re your friends. You can mess up with us, as long as you like us when we mess up.” He looked at the others. Mon was sitting up slowly, and nodding. “Well, I’m not sure Jo ever messes up. But I know I do a lot.”

“You would not believe the number of whoopings I get.” Mon said, smiling. “I pretty much deserve them. Dad says I have a lot of energy. That’s why he helps me swim, it tires me out and I don’t misbehave so much.”

“I...I don’t have time to misbehave.” Jo said quietly. She looked at her shoe. “I just go home and plug my corder into the large screen monitor my parents bought me. That way I can see what happened during the day.”

Al looked up. She smiled. “Is it weird that all of my friends are as weird as I am?”

“I’ll be weird with you guys.” Jo said. Wilbur and Mon nodded.

I would say that as long as each character has their own "tone of voice" and quirks, they should be easy to tell apart from the others.

That being said, it looks like you're throwing a lot of characters around, which can be dangerous if you want the reader to stay engaged and prevent the characters from melding into one another. It can be done, of course, but you have to be careful about it.