Canon

[Sky Shadow]

We can still have Soundwave take over the Decepticon forces when Megatron and the Nemesis dissappears with the Ark,

I'm guessing you mean Shockwave (since Soundwave is usually on the ship with Megatron.)

Nemesis and the Ark leave Cybertron in say... 1800AD (our time). They go through a wormhole/temporal anomoly thing and are taken back to several hundreds of thousands of years ago and crash on Earth, into the mountain and lay dormant until it explodes in 1985 and start G1.

This seems unnecessary and too derivative of Beast Wars. Also, one of the poignant aspects of the G1 comics is that Optimus Prime crashed the Ark on Earth was because it had no signs of life and thus he was responsible and guilty for bringing his war to Earth. Even assuming that Prime's idea of life is pretty narrow, it makes him even more ignorant if he decides that a planet covered in roads and the occasional monolith is uninhabited.