これを試してください:
SELECT t.*, cnt
FROM (
SELECT team_id, COUNT(*) AS cnt
FROM (
SELECT player_id, MAX(id) AS mid
FROM player_team
GROUP BY
player_id
) q
JOIN player_team pt
ON pt.id = q.mid
GROUP BY
team_id
) q2
JOIN team t
ON t.id = q2.team_id
ORDER BY
cnt DESC
LIMIT 50
player_team (player_id, id)
にインデックスを作成します (この順序で)これが高速に機能するため。