I had the same doubt... the A3000 is a GREAT machine but it doesn't offer AGA so you can't run all games.
In the end this has been my choice:
- A3000 + OS 3.9 (060/50, 128MB, CV64 4MB, Toccata, Ariadne, MP3@64, CD-R, ZIP...) for a definitive Amiga Classic experience. I can do everything with it!
- A1200 + OS3.1 (030/50 + SCSI, 32MB) just for WHDLoad, demos and gaming
In my opinion, except for the lack of AGA, the A3000 is the best Amiga ever built... but the A1200 in its original case is amazing for gaming. I consider it the definitive Amiga game station :-)
In short, you have to use both :-D
Alex