Ensuring relevance/believability are key to stories/characters and magic/superpowers. When reading, I become fully immersed in the fictional world that if a power/ability appears 'just for show', the book's credibility weakens to me and I am cautious/fearful any new aspect that is introduced will also end up being a pointless trait.
Though, I do enjoy when powers and their purpose are witheld, not discovered by the hero until the end, are the cause of the conflict to start with or not explicitly described as monumental to the plot.
Mix it up a bit, present the abilities as so amazing that the reader believes it's vital to save the day. However, give that power an unusual use by those who possess it, like breathing fire to grill toast! The cool power has a 'reason' to be there, it's unexpected and could add intrigue/humor/character insight etc.
Perhaps, re-purposing the lower/higher spectrum powers like that, could provide a quirky twist to your novel and maintain appeal.
I also struggle with this in my own writing. I mentally justify those replaceable aspects because of the coolness factor and I loved writing and showing it off... Impressed by my creative pizzazz like, far out! My world and creatures are super duper awesome because they have 17 different powers, shoot fireballs from their eyes while reading minds as they fly around the streets with glowing skin!
Obviously, a silly example but adding the superficial drama without reason leads me off track and dilutes my initial plotline. I just step back and re-trace my progress. My personal methods include:
Copy and paste! Re-Draft, move sections into different chapters/timelines or write a few versions-eliminate/alter/combine aspects. Replace the ability for another to see where it could go. Or just delete the lot as if it was never there!
Backstory check. In my own writing, I like the powers to be:
-Consistent with my created story/world history.
-Believable, not too absurd in comparison to other elements.
-Memorable, are characters and powers easily distinguishable by the reader or will it be confusing to follow who does what?
-Relevant, serving purpose to plot/conflict/character/theme etc that is clearly understood by the reader.
Good old pen and paper. Brainstorming! Word association techniques especially help me when cutting/changing/keeping the superficial studd. I challenge my use of language/words/phrases, weed out stereotypes/connotations or realise opportunties to incorporate the aspects with relevance I couldn't see before! E.g. Shooting eye fire-flame-heat-hot-warmth-snug-love... A potentially destructive power becomes a healing power of warmth and nuturing!
Seek feedback. Find someone (who can be relatively objective) to provide constructive critiscm. They could read your draft and comment. I like informal sessions, explaining a brief rundown plot etc like, "in X world, X exists and can do X magic..." and so forth. I have had good breakthroughs with friends, particularly when they aren't a fan of the genre, a writer or creatively-minded. Our opposite tastes and opinions have come together to help shape/recreate my story. I find this so valuable and a great creative outlet.
As I said, these are my personal steps to help shape believable plots where fantasy/magic etc is involved. It can be tricky to seamlessly concoct a believable fantasy tale with flashy superpowers to engage the YA reader. Relevance is still key though, avoiding cliches and bulking up prose with useless aspects can be at the expense of important plot devices/storytelling/character-building etc.
All of the above are basic techniques that can be applied any time. But whenever I get carried away in my world-building etc, instead of complicating it further by trying to create meaning/add information to justify aspects, it's a great to take a little bit of time and just simplify the process.