Brain-computer interfaces (BCIs) are systems that enable a person to interact with a machine using only neural activity. Such interaction can be non-intuitive for the user hence training methods are developed to increase one's understanding, confidence and motivation, which would in parallel increase system performance. To clearly address the current issues in the BCI user training protocol design, here it is divided into introductory period and BCI interaction period. First, the introductory period (before BCI interaction) must be considered as equally important as the BCI interaction for user training. To support this claim, a review of papers show that BCI performance can depend on the methodologies presented in such introductory period. To standardize its design, the literature from human-computer interaction (HCI) is adjusted to the BCI context. Second, during the user-BCI interaction, the interface can take a large spectrum of forms (2D, 3D, size, color etc.) and modalities (visual, auditory or haptic etc.) without following any design standard or guidelines. Namely, studies that explore perceptual affordance on neural activity show that motor neurons can be triggered from a simple observation of certain objects, and depending on objects' properties (size, location etc.) neural reactions can vary greatly. Surprisingly, the effects of perceptual affordance were not investigated in the BCI context. Both inconsistent introductions to BCI as well as variable interface designs make it difficult to reproduce experiments, predict their outcomes and compare results between them. To address these issues, a protocol design standardization for user training is proposed.