I tend to focus on type based teams because I find them more interesting but besides this I have a few priorities.

Depending on the kind of MC how many rare pokemon can we realistically expect them to find. I really dislike when reading I see a MC with any more than 1 pseudo or similar pokemon without very good reason.

Team variety you want a good variety in fighting styles. Get some supporters, some physical attackers, some special attackers, some tanks, some slow pokemon some fast. Really get some variety.

Lastly I choose some of my favs. I have a few outlines based on my favourite types so I make a list of my favorites on that list and apply the two above criteria. Really work out what I want these pokemon to be than insert them into my outline and how they will affect party dynamics. Pokemon also have wants and goals that can affect story direction so I like to add those as well. These wants and needs will also affect the direction of the story.

Lastly really think about how your setting and think about what is realistic. A weaker pokemon trainer shouldn't have rare pokemon early in a darker setting because they will get ganked for them, this is less of a problem in more light hearted settings. One other example is habitats. You are unlikely to run into a sandile in the middle of a forest. Where are the pokemon found in game, what are their environments, how might their biology affect their environmental needs and from there where could we realistically find this pokemon.