You can hate me for this, but Jojo's Bizarre Adventure parts 3, 4, 5, and 6 could probably be used as an example. Now for part 3 and 5 that was just the protagonist getting the same power as the villains/ becoming stronger (more OP) than them, parts 4 and 6 actually had underpowered characters outsmart the villains through tedious planning, leading to them being defeated. Some of the villains who had any form of time manipulation in the series were mostly cocky/arrogant, making them toy with the protagonists first before taking them seriously, which backfires horribly for them in the end.
For my ideas though, the easiest thing to do is make them more fatigued depending on how much of the power is used. If they use it often then they'll get tired quickly, but if they use it sparingly then they won't be AS tired.
Another idea is that they would unintentionally leave an opening for their opponent while fighting (assuming there will be any fights). Just like in games that punish you for hitting a character that did a perfect block/ hitting a character while defending, the time-based character can create an opening for their opponent like that and then they can have a chance to fight them before the time-based character can retaliate.
A lame one is having their time power be connected to a source (like Super Sonic with the Chaos Emeralds and rings), with the power source doubling as a generic main MacGuffin for your series.
For a last idea, make the character have other strengths than just time manipulation. Time powers can easily be overpowered, but they don't have to be a main thing the character has to be strong. This doesn't mean that the time thing should be weak while other attributes should be buffed, it just means you have to consider what the character needs to make the time power a reliance while at the same time making sure that's not the only they have going.
I hope these help you out, if you are looking for more stuff then try searching for help in the writing forum.
NoskynkGyesk
Some ideas i see, The idea of a Paradox that can erase them for the face of the universe
NecroNovaNG
Thatd be great to incorperate as a joke, if it wasnt for the fact my story is serious lol