GenAI for Systems: Recurring Challenges and Design Principles from Software to Silicon

Generative AI is reshaping how computing systems are designed, optimized, and built, yet research remains fragmented across software, architecture, and chip design communities. This paper takes a cross-stack perspective, examining how generative models are being applied from code generation and distributed runtimes through hardware design space exploration to RTL synthesis, physical layout, and verification. Rather than reviewing each layer in isolation, we analyze how the same structural difficulties and effective responses recur across the stack. Our central finding is one of convergence. Despite the diversity of domains and tools, the field keeps encountering five recurring challenges (the feedback loop crisis, the tacit knowledge problem, trust and validation, co-design across boundaries, and the shift from determinism to dynamism) and keeps arriving at five design principles that independently emerge as effective responses (embracing hybrid approaches, designing for continuous feedback, separating concerns by role, matching methods to problem structure, and building on decades of systems knowledge). We organize these into a challenge--principle map that serves as a diagnostic and design aid, showing which principles have proven effective for which challenges across layers. Through concrete cross-stack examples, we show how systems navigate this map as they mature, and argue that the field needs shared engineering methodology, including common vocabularies, cross-layer benchmarks, and systematic design practices, so that progress compounds across communities rather than being rediscovered in each one. Our analysis covers more than 275 papers spanning eleven application areas across three layers of the computing stack, and distills open research questions that become visible only from a cross-layer vantage point.