Yes, bgsjust it will be slow for an 030/28, but as you say you can configure it to run a bit faster. I won't change the default settings to be used for a low end Amiga the same way that I don't enable some programs in the WBStartup that need a fast CPU, I use an average configuration. Of course it isn't thought in using 4 colors only, not even 8, but in fact you could try with 8. You should explain what graphical options are different from the previous WB and where do you have any problem (maybe you are talking about using Magellan instead of WB?), but better if you use the right place, as the support of AmiKit Real is on EAB, here http://eab.abime.net/showthread.php?t=67562
It boots and runs right with 4 colors too, so I don't know what do you say about the screen "very low res selected at startup with 4 colors.". If you think that it was set as default by AmiKit, remember that the screen mode it uses when booting is the one you were using on your OS3.9 BB2, so it only can be you that set up 4 colors and whatever screen mode.
To change the background you have to make a right click on screen, Settings, Environment, Background. But it would be better if you install Copper-Demon http://aminet.net/package/util/wb/Copper-Demon
and you use it for windows at least. I'm planning to add it to a next update.
You could recover all the fonts taking them from OS3.9 and adding the ones of the complete AmiKit Real install.
If you use Workbench instead of Magellan it will be a bit faster too. You just have to click on MorpheuZ (in Amidock, in the StartMenu on the Tittle bar in Applications, or also in AmiKit:Prefs/Presets/AmiKit/MorpheuZ and select to Change Environment.
Thanks for asking.