Any aftermarket system would be better than the Shaker system, if it was properly installed. (Easier said than done). The best thing about the Shaker 500 system is that it has enclosures in the doors for the door subwoffers. Ported enclosures. The subwoffers occupying those enclosures are low quality. I doubt that they have a real crossover network. Probably just caps and chokes.
The Shaker 1000 system has two more small subwoffers in the trunk. They are not 10" subs. They are six or maybe 8" subs. Poor qquality. Ford is saying that the 10 speakers in the 1000 system are better speakers than the 8 in the 500 system. They probably aren't much better, but I don't know.
If you could replace the speakers in the door with JLs or something you'd have a better system. If you could get your own amp to power them off Fords head unit, you'd have a much better system. If you threw the whole thing out and just kept the ported subwoffer enclosures in the door, you'd have a much better system, probably not much more than another $600. You could get a better system for $600 from the base system, too.
But you'd have to open, cut, snip, solder, whatever. Just leave your Shaker 500 alone, and forget the Shacker 1000, I'd say.