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The trails at Alishan are completely different than those in Fenqihu. Which ones you prefer is a matter of taste but I saw both in 2017 and definitely would not miss the ones at Alishan.
Fenqihu trails are wilder and less obvious than those at Alishan that are more manicured in a sense. Think of it like a giant city park with a mountain in the middle. The trails at Alishan are impeccably maintained with wooden paths and stairs, facilities along the way and many interesting stops, including various temples and gardens. It also gets quite crowded there, the most I have seen at a National Park in Taiwan.
On the other hand, around Fenqihu, the trails are much less visited and you can be alone much more easily. While there are some landscaped paths, most of them are just a narrowly cleared paths. There are a few sights of note but much fewer than at Alishan. Do get your food at Fenquihu though, it is really good. Mind that things close quite early there.