@Apache2k
Yes the OCS and ECS Amigas use up to 16 colors only in Highres Interlaced mode. I think this is quite fine and it works for me on an A600 with 68030 33mhz and 32mb of ram. What you really should add is:
VisualPrefs
MagicMenu
ToolsDaemon
MUI
to reduce the flickering seriously. Also dont settle for less, get the 3.1 Roms, not the 3.0! and get the MEGACHIP for 2 megs of chipram.
the 68040 is good and I guess a gfx card is good too. I have never used a gfx card and dont plan to as I mostly do video and dont want my NTSC compatibility screwed up. I love my setup as it all runs in Video modes (704 x 480) or so. I also have an A2000 with 68040 and Megachip
Also, you could run WB in 32 colors if you put the resolution in LoRes (320 x 200) with autoscroll, and it could look nice with the right icons and visual prefs etc..