Urban bus transit agencies need reliable, network-wide delay predictions to provide accurate arrival information to passengers and support real-time operational control. Accurate predictions help passengers plan their trips, reduce waiting time, and allow operations staff to adjust headways, dispatch extra vehicles, and manage disruptions. Although real-time feeds such as GTFS-Realtime (GTFS-RT) are now widely available, most existing delay prediction systems handle only a few routes, depend on hand-crafted features, and offer little guidance on how to design a scalable, reusable architecture. We present a city-scale prediction pipeline that combines multi-resolution feature engineering, dimensionality reduction, and deep learning. The framework generates 1,683 spatiotemporal features by exploring 23 aggregation combinations over H3 cells, routes, segments, and temporal patterns, and compresses them into 83 components using Adaptive PCA while preserving 95% of the variance. To avoid the "giant cluster" problem that occurs when dense urban areas fall into a single H3 region, we introduce a hybrid H3+topology clustering method that yields 12 balanced route clusters (coefficient of variation 0.608) and enables efficient distributed training. We compare five model architectures on six months of bus operations from the Société de transport de Montréal (STM) network in Montréal. A global LSTM with cluster-aware features achieves the best trade-off between accuracy and efficiency, outperforming transformer models by 18 to 52% while using 275 times fewer parameters. We also report multi-level evaluation at the elementary segment, segment, and trip level with walk-forward validation and latency analysis, showing that the proposed pipeline is suitable for real-time, city-scale deployment and can be reused for other networks with limited adaptation.