Which would you be more likely to let go?
I had a really nice A2000 back in the day.
PP&H 040/28MHZ, 32mb 32bit ram, CV643D, GVP4008 SCSI with GURUROM (4MB RAM), Hydra Ethernet.
My ancient revision 4.0 A2000 was super stable and quite fast once the Kickstart and workbench was relocated to 32BIT ram. It was actually quite a bit faster than a stock 4000.
Everyone I knew with 3000 and 4000s were always needing some magical combination of busters and dmacs to get a stable system. At the time said I was very happy not dealing with that drama, but sure I would have traded my 2000 for a similarly configured 3000

Between the 2000 and 3000 I'd still pick the 3000, partially because I have never had one.
Other than that, the faster Z-III bus and built in flicker fixer would be the selling point.
I really don't see one significantly better than the other. The are both pretty ugly on the outside bu today's standards - not sleek and modern like the wedge computers

If you are not doing this for financially motivated reasons, Have you ever thought of unloading both and putting together a 4000?
Everyone comments on how worthless of an upgrade AGA was.
I remember reading about the specs on ECS when it came out and was truly underwhelmed. About the only good news there is that existing computers could be upgraded.
AGA on the other hand is a significant improvement with 8bpp in any mode and 4X the speed.
Lots of cool stuff will use AGA but not a GFX board. Paint programs, etc. I love watching AGA demos on my 1200
