Ups and downs for both:
3000 benefits:
Zorro slots for easy expansion.
Built-in scan doubler
Comes with 030 as standard
SCSI interface for CD ROM and hard drive
1200 benefits:
Many cheap accelerator cards available
PCMCIA slot.
IDE slot.
AGA.
In the end, for heavy expansion its easier to start with a 3000, since towering a 1200 is a fair amount of work, cost and fuss.
If you want RTG, its pretty much 3000 or towered 1200 anyways.
On the other side, its easier to fit simple IDE CF options to the 1200, you get PCMCIA for networking and file transfers, and you get AGA, which opens some software options.
You forgot a few things here.I love the 3000 and 1200 but...
The 3000 will likely have a 030/25, old buster 7,9 if your lucky. Need upgraded for zorro3 operation,need a updated scsi chip(not always). The 3000 will probabaly need 3.1 roms,it will have a old dmac2 and ramsey 4 also. it uses more expensive zip ram. it has a 030/25 (in most cases),no place for cd/dvd rom.Of course if you can find one cheap with all this your golden.
The 4000 makes most sense, it has a 040/25 stock and at least 3.0 roms,can take 16MB of easy/cheap 72 pin simms,is AGA,has latest ramsey etc. chips(buster11 except some came with buster 9-which is still better than buster 7 which has broken zorro3),it has a slightly better power supply,room for a cd/dvd. Can add a pal/ntsc switch if needed. 4000's Can usually be picked up in the $300-500 usd range in stock 040 form..
The 1200 makes the least sense. you would need a tower, accelerator,bus board expansion,new power supply,etc. its pcmcia is a nice thing,but its ide is unbuffered and slow.by the time you buy all these addons its will be as much as a 4000 and still not be a fast.Bringing a 1200 up to this spec would cost way more and still be slower in most cases.