I think it just comes down to how much you want to hike. I was really looking at the Choquequirao trek since the Inca Trail is normally sold out when trying to do things last minute.
We just did not have time so we decided to skip any hike and just take the train. It was still a lot of hiking around M.P. and up to the peak.
Also, we took the bus up and that was a great decision as I am not sure if I could have made the peak if I included the hike up to M.P.
I know nothing about any of the trekking companies and nothing about Rainbow Mountain.