Recent advancements in Large Language Models (LLMs) have greatly extended the capabilities of Multi-Agent Systems (MAS), demonstrating significant effectiveness across a wide range of complex and open-ended domains. However, despite this rapid progress, the field still relies heavily on empirical trial-and-error. It lacks a unified and principled scientific framework necessary for systematic optimization and improvement. This bottleneck stems from the ambiguity of attribution: first, the absence of a structured taxonomy of factors leaves researchers restricted to unguided adjustments; second, the lack of a unified metric fails to distinguish genuine collaboration gain from mere resource accumulation. In this paper, we advocate for a transition to design science through an integrated framework. We advocate to establish the collaboration gain metric ($Γ$) as the scientific standard to isolate intrinsic gains from increased budgets. Leveraging $Γ$, we propose a factor attribution paradigm to systematically identify collaboration-driving factors. To support this, we construct a systematic MAS factor library, structuring the design space into control-level presets and information-level dynamics. Ultimately, this framework facilitates the transition from blind experimentation to rigorous science, paving the way towards a true science of Collective AI.