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First get an idea of the meta you want to play, OU, VGC, Ubers or whatever, and learn what is prevalent in that meta and work your team around being prepared for it
A lot of being able to see weaknesses in a team comes from experience
Pic related was my notes when I made a Venusaur/Heatran + M-manectric voltturn team, that was scrapped after I found out manectite is still unavailbe