This study tests the Bottleneck Hypothesis (BH) that functional morphology presents the greatest difficulty in second language acquisition by examining Chinese English as a foreign language (EFL) learners' knowledge of both functional morphological properties and core syntactic properties across three language proficiency levels. Specifically, this study compares Chinese EFL learners' grasp of subject-verb agreement (a functional morphological property) vs. their grasp of the syntactic formation rules (properties) of WH-questions including WH-movement, WH-"do"-insertion (i.e. the insertion of the auxiliary do), and WH-"do"-inversion (subject-auxiliary inversion): three core syntactic transformation rules. Analyses of the experimental results using generalized mixed-effects models yield complex results that generally support the BH. While subject-verb agreement was found to be persistently more difficult than WH-movement and WH-"do"-inversion, it was shown to pose essentially the same level of difficulty as WH-"do"-insertion due to the fact that the latter also involves the application of the functional features of SV-agreement and tense, i.e. the high level of difficulty of WH-"do"-insertion likely lies in its accompanying application of functional features. Possible explanations for the complex results and their implications are discussed.