With figures like the skeletons or Phemera Omega or Storm Golems, I definitely think the sanding approach is the way to go. The bases look good and are nearly identically-sized to the classic medium Heroscape Bases. No need to go through all the effort of rebasing, in my book.
For Zaeus and the VBDs, it's a slightly stickier question, because the bases they are mounted on are larger - basically the same size of the D3 large round bases. If it bothers you to have a medium figure on a large base, then I could see rebasing those. Personally, I don't think it's a big deal, though.
For Omegacron, I also use an exacto knife. One suggestion I have is to let the figure sit in a pan with some boiling water for a minute before you rebase. This will soften the plastic and make your job easier. This trick helps soften the basing materials of all minis, although it's less effective on Huge D&D figures (which have stiffer bases than small/medium/large D&D figures).