I wonder how much 3.5/3.9 code they did manage to re-use given all the legal issues with H&P; I know that Amidock is a completely new application, for example, but I'm guessing they somehow managed to get the code for things like ReAction...
A few things are are missing. Arexx is 68K, and likely to remain that way since they only had a license to the 68K source code, and can only go as far as debugging that same source code. Hyperion brought Python in, but it just doesn't look as easy as AmigaDOS and Arexx scripts. Not to matter, as even if Arexx gets bumped off, programs can still support Arexx ports and commands. Since it is just a standard message port and messages in Arexx format; just a "string in a structure" really, so easily kept going.
The Installer was lost, although they have made their own for certain things; thus the OS4 installer can't be used to install OS3.9 programs that make use of it's multimedia or other features for instance.
The Printer modules were lost. They had to spend time reimplementing features there and not all were put in. So the OS4 printer.device is not perfectly backwards compatible to the OS3.9 one .
I thought Palette used to be 68k, it's now native. IIRC it had some screen colour bug. It's still not right, as it looks dated and has no colour wheel? :-? Perhaps that was the sacrifice for becoming native.
There there is Unarc, some decompressors are 68k.
The Shell. Well I never liked the ones used to replace it in the past. And always thought they should just bite the bullet and get the sources to KingCON. Well now I guess it's too late and the Shell we have is slightly better than what we had in OS3 and 100 times better than what you get in WindowsXP!
From my above descriptions it would look like AmigaOS4 is a big mess! I would have liked a more cleaner rebirth to the Amiga, but it was pulled apart after Commodore already broken it. so this is what we ended up with. It still here at least. :-)