Deep learning has significantly contributed to medical imaging and computer-aided diagnosis (CAD), providing accurate disease classification and diagnosis. However, challenges such as inter- and intra-class similarities, class imbalance, and computational inefficiencies due to numerous hyperparameters persist. This study aims to address these challenges by presenting a novel deep-learning framework for classifying and localizing gastrointestinal (GI) diseases from wireless capsule endoscopy (WCE) images. The proposed framework begins with dataset augmentation to enhance training robustness. Two novel architectures, Sparse Convolutional DenseNet201 with Self-Attention (SC-DSAN) and CNN-GRU, are fused at the network level using a depth concatenation layer, avoiding the computational costs of feature-level fusion. Bayesian Optimization (BO) is employed for dynamic hyperparameter tuning, and an Entropy-controlled Marine Predators Algorithm (EMPA) selects optimal features. These features are classified using a Shallow Wide Neural Network (SWNN) and traditional classifiers. Experimental evaluations on the Kvasir-V1 and Kvasir-V2 datasets demonstrate superior performance, achieving accuracies of 99.60% and 95.10%, respectively. The proposed framework offers improved accuracy, precision, and computational efficiency compared to state-of-the-art models. The proposed framework addresses key challenges in GI disease diagnosis, demonstrating its potential for accurate and efficient clinical applications. Future work will explore its adaptability to additional datasets and optimize its computational complexity for broader deployment.