While recent Flow Matching models avoid the reconstruction bottlenecks of latent autoencoders by operating directly in pixel space, the raw pixel manifold provides little explicit semantic organization, making target-specific transport directions difficult for a shared finite-capacity vector field to distinguish. When different transport requirements are locally entangled in this way, their learning signals can interfere and hinder optimization, a phenomenon we refer to as trajectory conflict. To alleviate trajectory conflict while preserving direct generation in pixel space, we propose Waypoint Diffusion Transformers (WiT), which introduces explicit semantic routing into pixel-space generation. WiT structures pixel-space prediction through compact semantic waypoints projected from pre-trained vision representations, providing a semantically organized intermediate representation that complements direct pixel prediction. During ODE integration, a lightweight Waypoints Predictor dynamically infers the semantic waypoint from the current noisy state, and the predicted waypoint continuously conditions the primary Pixel Space Generator through our Just-Pixel AdaLN mechanism. This spatially varying semantic modulation reorganizes the finite-capacity learning problem and helps the model preserve target-specific transport directions while retaining generation entirely in pixel space. Experiments on ImageNet 2012 demonstrate consistent improvements over strong pixel-space baselines across model scales, with WiT-H/16 achieving an FID of 1.79. Code will be released at https://hainuo-wang.github.io/WiT.

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