WiFi-based indoor positioning has attracted intensive research activities. While localization accuracy is steadily improving due to the application of advanced algorithms, the factors that affect indoor localization accuracy have not been sufficiently understood. Most localization algorithms used in changing indoor spaces are Angle-of-Arrival (AoA) based, and they deploy the conventional MUSIC algorithm. The localization accuracy can be achieved by algorithm improvements or joint localization that deploys multiple Access Points (APs). We performed an experiment that assessed the Test Point (TP) accuracy and distribution of results in a complex environment. The testing space was a 290 m2 three-room environment with three APs with 38 TPs. The joint localization using three APs was performed in the same test space. We developed and implemented a new algorithm for improved accuracy of joint localization. We analyzed the statistical characteristics of the results based on each TP and show that the local space-dependent factors are the key factors for localization accuracy. The most important factors that cause errors are distance, obstacles, corner locations, the location of APs, and the angular orientation of the antenna array. Compared with the well-known SpotFi algorithm, we achieved a mean accuracy (across all TPs) improvement of 46%. The unbiased joint localization median accuracy improved by 20% as compared to the best individual localization.