The last version of the 90/2.8 is outstanding - outperforming the 1st close up, etc. That said, your 1st version 90/2.8 should be sharper than the 90/2 pre-apo until about F5.6 or so when they should start to look similar (in resolution terms only).
Bokeh on the 90/2 would be considered smoother/more buttery and it has that Mandler 'glow' (like the 80 Summilux) vs the 90/2.8 which is why the former and the 80 are so well regarded as a portrait/'artistic' lens. Take a close look at your lens, etc if you think it's resolution seems 'off' vs what you're seeing here at the same apertures.
As you suggest, the 90/2 APO is a whole other kettle of fish.