When I purchased my first machine, I bought a huge thread set off of Ebay. When I bought my most recent machine (a Pfaff) it would not stitch with the thread I had. It only likes the Robison Anton or other expensive thread(lol).
So my recommendation is try out a few manufacturers first. As far as colors - From the large lot I purchased, I used a handful a lot and the rest were never opened. I now purchase the colors for my designs as I need them. I always keep the usual primary colors on hand as well as Christmas red and green and other colors grow as I need them.