Apple Daily says there have been "numerous mishaps" and "no outstanding achievements" during Mr Ma's term.
Mr Ma's spokesman denies any party-political bias among prosecutors, and insists the president respects judicial neutrality.
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In July the two firms made peace, but not before Mr Ma suggested publicly that Yahoo!
Mr Ma has not yet won his party's nomination, and indeed has stood down as chairman.
Mr Ma is still seen as the party's best hope of winning the election.
Since taking office in 2008, Mr Ma has worked hard to improve cross-strait ties.
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Mr Ma's standing, he argues, depends on whether they can actually revitalise the economy.
But Mr Ma will be keen to distance himself from any more cabinet embarrassments.
That would hardly be in keeping with the clean-guy image of Mr Ma, a Harvard-trained lawyer.
But, at the least, Mr Ma managed to halt the slide in his popularity.
That sets Mr Ma apart from Mr Lee, for whom reunification is no holy grail.
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So Mr Ma has to balance his economic romance with China with political aloofness.
Much as it likes Mr Ma, China will not accept the legitimacy of his government.
Beijing-watchers in Taiwan say senior Chinese officials differed about how to respond to Mr Ma's request.
After their respective inaugurations, Mr Ma said, neither he nor his vice-president would be likely to visit.
Mr Ma said that overlapping of duties within various ministries had often led to officials passing the buck.
BBC: Travellers at the Beijing West Railway Station, Jan 2013
But Mr Tsai acquitted Mr Ma, and gave an aide involved in the abuse a year in jail.
Ms Tsai also accused Mr Ma of upsetting the regional balance of power, alarming Japan and South Korea.
Business Times and Economic Times says Mr Ma has failed to satisfy public expectations mostly on economic governance.
Mr Ma's predecessor, Chen Shui-bian, had angered China with moves towards formal independence, and relations had been severely strained.
Mr Ma has promised that when the deal is negotiated, the wording will not compromise the island's political stance.
The outcome of the election was not an overwhelming vote for Mr Ma.
In private, DPP leaders admitted to him they thought Mr Ma the victor.
However, Central Daily News says it is unfair to hold Mr Ma entirely to blame for a sluggish economy.
Mr Ma's own reputation for competence has also been damaged by his government's slow and muddled response to the crisis.
At the least, argues Hsu Yung-ming at Taipei's Soochow University, the scandals may affect Mr Ma's choice of running mate.
When China's trade ministry asked Mr Ma to set up ChinaMarket, 4, 500 companies joined before he ran a single advertisement.
But Mr Ma believes most people could afford water at a realistic price, and they would use it more efficiently.
However, Mr Ma's hotel has not displayed Taiwan's flag and it is only flying outside Taiwan's embassy in the Holy See.
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