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Creator Backlash: Bungiewas not happy about their IP being used by another developer for a different genre. As such, they had little participation with the game. However, they seem to have eventually made peace with it; the "Dr. Halsey's personal journal" booklet which came with the Limited/Legendary editions of Halo: Reach and Halo: Contact Harvest contain a fair number of direct references to Halo Wars.
Why the game became a Halo title. The order to turn it into one was expected to speed up production, but actually pushed back development a full year. The execs thought it'd be easy to just port in Halo models from the previous games, not realizing that there's a big difference between a full-scale tank model for a high-res FPS and a tiny differently proportioned one for an RTS, not to mention all the new units that had to be made to fill gaps in the meta-game.
Mark Worden (Iron Man) is the Brute Army Commander.
Throw It In: Graeme Devine, the lead writer, made an entire press guide for the planet Arcadia. Bungie's writer Joseph Staten liked it so much that he included a mention of Arcadia in Halo: Contact Harvest.
What Could Have Been: The control scheme was designed separately for an original property, yet undecided at the time. Microsoft was not confident about the sales of a new series as a console RTS, so they demanded for it to be a Halo game instead.
Incidentally, this game isWhat Could Have Been for the Halo series as a whole. It was originally planned as a strategy game when the game was still anticipated to arrive on Macs.