Stargardt disease is the most common form of juvenile-onset macular dystrophy. Spectral-domain optical coherence tomography (SD-OCT) imaging provides an opportunity to directly measure changes to retinal layers due to Stargardt atrophy. Generally, atrophy segmentation and prediction can be conducted using mean intensity feature maps generated from the relevant retinal layers. In this paper, we report an approach using advanced OCT-derived features to augment and enhance data beyond the commonly used mean intensity features for enhanced prediction of Stargardt atrophy with an ensemble deep learning neural network. With all the relevant retinal layers, this neural network architecture achieves a median Dice coefficient of 0.830 for six-month predictions and 0.828 for twelve-month predictions, showing a significant improvement over a neural network using only mean intensity, which achieved Dice coefficients of 0.744 and 0.762 for six-month and twelve-month predictions, respectively. When using feature maps generated from different layers of the retina, significant differences in performance were observed. This study shows promising results for using multiple OCT-derived features beyond intensity for assessing the prognosis of Stargardt disease and quantifying the rate of progression.