Contrast is higher on the 105MC than the 105/2.8 AiS. The newer lens also has somewhat better control of chromatic aberrations but here should be mentioned the old AiS was among the better of Micro-Nikkors in this regard. The latest of the 105 Micro-Nikkors, AFS 105/2.8, displayed way too much chromatic nasties for my taste and had the doubtful honour of being the only Micro-Nikkor I quickly sold off after a few month's use.
In terms of size, the Z lens is much bigger but goes to 1:1, however if one wishes to do 1:1 the old lens has to add extension (PN-11 or similar) so extends significantly in length. PN-11 has a rotating tripod collar whilst the 105 MC has none in the stock version. There is a third-party collar (iShoot ZMC105) that is sturdy and well made, but quite expensive and have several issues. Firstly, it conflicts with Z9, secondly it only allows vertical shooting as the collar isn't rotating. The latter problem can easily be overcome by 5-10 minutes of judicious Dremel work, though, but the incompatibility with the Z9 remains.
For sheer image quality, the new Voigtländer 65mm f/2 APO-Lanthar blows away both Nikkors. It might even be *too* sharp for some applications, a statement made both by myself and Michael Erlewine. The 65 APO sells for around $850 so is cheaper than the 105 MC. It only goes to 1:2 like the old 55mm Micro-Nikkors thus one needs to use extension on it. However it has full electronic communication with the camera and a rotating aperture ring that can be set to 1/3 or 1/2 stops. Workmanship is exemplary.