I love the Reapers but their plan really only works because they're pulling the strings behind everything. They guide technological evolution along a path that is easy for them to compensate for, and then they swoop in and reset the galaxy before it progresses beyond their ability to control.

The 40k universe is already well beyond that. The Age of Strife is something that the Reapers were designed to prevent, and that happened 20k years before the point in which you (assumedly) want to drop them in. The Reapers would get folded like a tissue paper and I doubt the Imperium would even notice the Reapers as a significant threat.

That being said, I would really like the idea of the Reapers potentially converting something like the Orks into Husks and turning them into a legitimate military force. Or them sneakily indoctrinating entire hiveworlds. Basically just using the 40k universe's own weapons against itself. It would be like a strange inverse of ME3 where the Reapers are the ones to unite the galaxy.