Geremie - I don't know of any software that can do what you describe. What you run up against is each manufacturer writing their own program that just covers their devices; there is no standard of interoperability.
There are some exceptions to this but it still falls short of true universality. I have an Animas Ping pump and also use the Dexcom G4 CGM. Animas has made a deal with Diasend, a web-based site that can integrate data from Animas, Dexcom, and many glucose meters. It works well for me but it too fences out users of many other brands of devices. It's part of what factors into my decision to stick with Animas. I'm sure that's what their marketing types intended.
What we need as a community is the ability to upload from any brand glucose meter, pump, and CGM to a system that can integrate that data all in one place so we all can start to extract useful information to help us win our individual D struggles. I would also like to be able to upload my pedometer or other exercise monitor and integrate into reports. Diasend does not do that.
And while we're at it, there should be one standard for uploading devices, either one standard cable or one standard wireless communication. This whole issue has been raised at various D meetings that manufacturers attend with PWDs but there's no apparent indication that the manufacturers are sympathetic with this need.