So my main character is reasonably intelligent, good at reading people, a decent battler and generally has received the goods of life in a basket from God.
What will, in my eyes, avoid making her a Sue is the fact that she still has struggles. Being new to pokemon training obviously means talent's only gonna get her so far. She has her convoluted reasons for doing what she does and they will be a driving force throughout the story - also, she's got some real personal issues on the side. Her starter pokemon isn't cut out for battling either, which is one momentum of the personal struggle side (but by no means an actual handicap to her battling strength; "she's strong but her pokemon sucks" would be too plain a reason - after all, she catches other pokemon, and she knows what she's doing when looking for strong ones). She also experiences issues with other people; the ups and downs of relationships gets to even the most socially and emotionally intelligent and mature of people, and that will be an important part of the story. Moreover, her opposition is more than strong enough for her - actually, she doesn't really stand a chance against the bad guys because, well, they are experienced and she is not. There's no way a rookie trainer could beat an experienced adult unless the latter used pokemon of lower quality than the rookie, that's just fact.
There's also a character on the good guy side who's strong enough to thrash a champion like they were, well, trash, whose strength is capably justified both through talents, battling experience and several personal reasons leading to the required drive and motivation to become someone like that.
So basically, make them have issues, struggles - they don't have to be flaws as much as they are emotions - real emotions, relatable emotions; emotions that makes sense within the context of the story, their personal story and their person. Not some cheap flaw or obviously contrived emotional issues; pick something you could relate to. Try and see them as a real person.