Jinnah faced extreme difficulties in the three-month-long grueling negotiations with the Cabinet Mission. The first of these was the continued delicate state of his health. At a critical stage of the negotiations, he went down with bronchitis and ran temperature for ten days. But he never gave up the fight and battled till the end of the negotiations.
Secondly, the Congress was still much stronger than the Muslim League as a party. "They have the best organized -- in fact the only well organized -- political machine; and they command almost unlimited financial support…they can always raise mob passion and mob support…and could undoubtedly bring about a very serious revolt against British rule."-- Mountbatten's "Report on the Last Viceroyalty".
Thirdly, The Congress had several powerful spokesmen, while for the League Jinnah had to carry the entire burden of advocacy single-handedly.
Fourthly, the Mission was biased heavily in favor of the Congress. Secretary of State Pethick-Lawrence and Cripps, the sharpest brains among them, made no secret of their personal friendship for the Congress leaders.
Wavell was much perturbed by Pethick-Lawrence's and Cripps's private contacts with the Congress leaders and the deference they showed to Gandhi.
Finally, Jinnah suffered from the disadvantage that it was the Muslim League, a minority party, which alone demanded Pakistan. The Congress, the smaller minorities and the British Government including the comparatively fair-minded Wavell with whom the final decision lay, were all strongly opposed to the partition of British India.