As regards digital source, Rega Apollo is far better than CD5003. There's no comparison at all!
Marantz CD5003 is a nice warm player but it sounds dark on mids and its top end is overmellow and lack resolution. Other fault is its mid-bass which may sound nice at first, but it's actually over-enphasized. Botton end is heavy, but could be tighter and better in timing.
If I had to buy an entry level CD, Marantz CD5003 would be on the top of my preferences, but it cannot challenge players like Rega Apollo or Arcam FMJ CD17
Concerning those amps, I've never heard the new Brio-R. It comes with a stylish new case but by taking a look at internal pictures I figure out it's not a huge step up from the old model despite its extra 200 pounds additional price. If I were you, I'd previously listen to Brio-R before taking it home.