Those races focused on local issues, and none of the offices has a say over cross-strait policy. But in the 2016 presidential and legislative elections, the divide between those who favor independence and those who argue for a future as part of China will play a more central role.

Some voters question economic cooperation because China has not renounced the possible use of force against the island. Others believe that the increased ties have not benefited most Taiwanese: While trade between the two sides has soared under President Ma Ying-jeou, wages have remained stagnant.

The trade pact has stalled in the legislature. As part of the compromise that brought an end to the Sunflower protests last spring, lawmakers are debating new rules for monitoring agreements with China before taking any further action on the deal.

Approval of the pact or any other deals with China seems unlikely for the remainder of Mr. Ma’s term, observers say. He stepped down as head of his party to accept blame for the Kuomintang’s electoral drubbing.

Beijing made little comment about the election outcome, but observers say cross-strait relations may become more complicated.

“Taiwan is going to be increasingly in the public eye because of growing tension with the mainland,” said Jerome A. Cohen, a New York University law professor who focuses on the region. “It will have implications for U.S.-mainland policy and for U.S.-Taiwan policy.”

He said he foresaw a period of increased acrimony in the region as the possibility for further cross-strait agreements diminished. But leaders of the opposition say such fears are overblown and based largely on the record of President Chen Shui-bian, the opposition leader who served from 2000 to 2008.