I would say regulations, grey areas, and language are the three main challenges. First, being unfamiliar with regulations might get you into trouble, such as fines. In addition, some regulations still limit certain rights that a foreigner can have.
Yet, this situation is improving since interest groups, SMEs and foreign chambers of commerce have been giving the Taiwanese government some pressure. Second, one has to know that what the regulation says is often a lot different from what is actually done and what is perceived as the norm. You might find yourself caught in dilemma, facing many grey-area situations. Last, whether language is a disadvantage or not depends entirely on what kind of industry you are in. It can be a disadvantage or it can have literally no impact on you at all.