I like the idea. I've already got an idea for two Flood Leaders and one Forerunner Leader. The Forerunner Leader would be 2401 Penitent Tangent from Halo 2. His units & buildings would be mostly Sentinel-based and include the iconic Aggressors, the Enforcers & scrapped Forerunner Tank from Halo 2, the Super & Protector Sentinels from Halo Wars 1 along with the Sentinel Factory building, Armiger infantry, the Forerunner Aardvark from the cancelled Halo: Titan MMO, and the Controller & Retriever from Halo Wars 2 as the Hero & Super Unit respectively along with the Sentinel Turret. I originally envisioned him as a UNSC Leader so he'd also have access to some of their assets.
The Flood Leaders would be composed of two "strains" as I call them: UNSC & Banished. As you can guess they would be mostly composed of infected units & buildings from the two main factions of Halo Wars 2 while also coming with some unique assets of their own. The UNSC Strain would include the Infected Spartan Hero Unit and the Flood Egg resource building while the Banished Strain would come with the Thrasher Hero Unit and the Carrier Form unit. Both however would make use of Flood Stalks. Flood Roots, & Flood Launcher buildings as well as Spore Mounds from mini-bases. They'd also share the Abomination as their Super Unit along with several of the Flood units introduced in Awakening the Nightmare. As for the Swarm & Bomber forms from Halo Wars 1, they'd become Leader Powers for the two strains.