I've always thought that the Separatists were too incoherent and "weak" villains.
How about introducing Dooku early on as the master of Maul (no "Darth", just Maul). And Dooku's personal flagship, from which he leads the nascent Separatist movement, could be the Invisible Hand.
An idea I had sometime ago was about basing Ep. II around a search for Doou and his flagship. In a sense a reverse situation of TESB, only this time it's the rag-tag Republic strike force trying to hunt down the large enemy ship.
The Clone Wars did something similar in the Malevolence arc.
As for blowing up, I believe a CGI shot with an overlaid explosion wouldn't be that hard.
Personally, I like the donut ship design (a lot, in fact) but it served its purpose in Ep. I. It looks like a floating hangar that dispatches troops or hauls cargo not a fast warship.
The Invisible Hand, on the other hand (sorry), looks like a fast and menacing ship that's made to fight and escape, if needed.