via: newsweek - panda politics
Taiwan Premier Frank Hsieh said the island was unlikely to accept the creatures because to do so would "compromise our sovereignty." The reasoning goes like this: Pandas are an endangered species, and under the Convention on International Trade in Endangered Species, pandas can only be lent—not given—by China to other countries. Taiwan has no pandas; the animals are native only to mainland China, where 1,590 live in the wild and 190 are being kept in zoos and breeding centers.
one reason i like taiwan president Chen Shuibian is that he is an honest man and always speak out what he thinks in his mind. this time he asks taiwan people to resiste the panda offer because "Whatever China says or does to Taiwan, it has only one purpose—to annex Taiwan", in Chen's eyes, these two cute animals are the "trojan pandas", so to speak.

in my opinion, the panda offer and similar exchanges of goodwill, information and people between the two sides will lead to exactly the opposite result - with more understandings of and sympathies towards taiwan people, mainland chinese will take a softer stance and become less likely to favor a reunification-through-force approach in the future.
messages like this, be it an intimidation from the mainland or demonization from taiwan, only works to sour the relationship.