A2000 w/ 060 speed?

[terminator4]

Amiga 2000 with 68060 Blizzard (or TekMagic) + RTG card is pretty much faster by at least 3-4 times imho than A3000+68030.  I think the speed won't be utilized fully by WHDload...  though the SCSI controller on those accel boards is better than the A3000 WD chip.   Also the Blizzard board will give you more memory.  If you have flicker fixer board in a2000 then you're settled.   A3000 is still nice machine though.  Advantage of A3000 is it has flicker fixer, scsi all build in, which way back in a day was themed: amiga done the way it should have been.  (compared to A1000 noscsi/flickerfixer and partly because A2000 2091 scsi board was a bit slow).
Having both of them is ok, but if you must choose do A2000+68060+RTG as its great for other tasks than gaming as well.  Assuming your A3000 has full memory 16mb, flicker fixer build in, its not a bad choice to run WhdloADgames.  I THINK your decision should be driven by cost.  Cost of 68060 is likely the same or close to cost of A3000???
I noticed everything redrawing faster on my WB with my 68060 than with 68030.
Lastly, Amiga 4000T (tower one) is the best one of them all.  Too bad its hard to find and costs quite a bit more than A3000 or A2000 with accelboard.

[terminator4]

while on topic of a2000...
Only rev 4 board is german made and it had issues.  
rev 4.x and 6 were designed in westchester, pa and produced in hong kong / taiwan etc.
All my Amiga 2000s don't say Made in germany so maybe you have something you picked up in europe?
I also have rev 4.3 A2000 board and thats cr*p compared to rev 6.x which has all the changes and fixes.  of all of them 6.2 and 6.3 and 6.4 are more desirable obviously.
I think A2000 was build at time when Commodore was doing ok, ok enough not to be cheap etc.  A3000 came in 1990 and I think by then Amiga/Apple were losign their edge to IBM Clones so some corners might have been cut (the case is very small similar to PC-ii or PC-iii that commodore was selling)