Not sure why you might be seeing a difference, other than possibly you have older USB micro cables? i..e not usb 2.0? Or they may just be low quality cables.
I have a mix of older Moto USB cables (from my Droid, Droid X and Bionic), as well as a few 3ft, 6ft and 12ft cables (labeled as USB 2.0 or Hi-Speed USB) that I got from Newegg.com (link depot) and the local Tiger Direct store (cables to go and another brand I forget the name of). At the office I have the cables that came with my Galaxy S2, S3, S4, S5, Note 2, Note 3, Tab 3 10.1" that I often use.
As long as the wall wort (or car charger plug) is 1A or higher, my X charges in the same amount of time no matter which of these cables I use.
If you order from Moto, pay attention to the shipping!! the highest cost shipping method is often selected by default.