Ok,i will get flamed for this but:
The A4000 is full 32bit across the board, the 1200 is not.
The A4000/040 blows the 1200 away stock machine to stock machine and here is why.
Internally a CDRW or DVD-RW,2 hd's and 2 floppies fit the A4000- The A1200 gets 1 HD and 1 floppy (yea,i know,u can hack a laptop dvd-rw internally) but this is hacking.
The A4000 comes with a decent 150W psu. A1200 is a crappy 20~ watt psu.
the 1200 is actually wider than the 4000,but not as deep or tall, so you could call that a draw.
the A4000 is AGA also
You can set a monitor on top the 4000.
The A1200 is 020EC(no mmu/fpu) 14mhz with 2MBram,the A4000 is 040/25 with full mmu/fpu 16MB ram on the motherboard.
comparing stock to stock machine, the A4000 ide is faster(040 helps),the ide in the 4000 is at least buffered.
You can technically make a A4000 quite a bit faster than the 1200 with the csppc. 604/233 blows the 603/240 out of the water.(not withstanding guys hacking bliz boards,i'm talking stock parts here).
CSPPC UWscsi screams,it pushes 20+MB/s on the crappies drives.blizzard is scsi2(10MB/s if your lucky).
The A4000 stock has a proper expansion bus,zorro3, not crappy slow clock ports and 50 dongles hanging off stuff to make it decent.Even the A1200 FastATA and such is a cpu pig,while the csppc scsi cranks along at full speed with low cpu usage(even a CS MKIII).
If you want to compare mediator in both models,the 1200 loses again for speed, its transfer window to the board is smaller i.e. slower..
The A4000 is easy to install a pal/ntsc switch also,so you can permanently switch easily between pal/ntsc-just 2 wires with switch to the jumper.
The A4000 comes with a clock.
A 16MB A4000 with stock 040 card(even the crappy A3640) is a way way way faster machine out of the box than a stock A1200,and still a bit faster than the 030/50mhz boards in the 1200(yes theres 040/060 boards,but dont forget the prices!). and as far as cost, expanding a 1200 these days just to meet the A4000 usually costs as much or more.
The A1200 pcmcia is a winner tho,very handy for cheap ethernet or Pcmcia/cf,i will give it that hands down.
A zorro3 deneb though will out do the subway in a 1200 speed wise by quite a factor.if u want to do this, you could argue a $5.99 ehternet dongle is the way to go in the A4000 and will be faster than 1200 pcmcia ethernet.you also get USB2 and a flashrom to install a ton of stuff in.The deneb would only run on the 1200 with a zorro board/mediator addon in slow z2 mode(2-3MB/s?).
The 1200 also wins portability,but then again the bulky psu is not convienient and should be counted,the A4000 psu is at least self contained in the box.The A4000 comes with a real on/off switch on the machine

There a indivision for the 4000 also.
If u price a expanded 1200 and a used 4000,i bet you the price comes out close(and i dont mean if someone gave u a pile of stuff free).
Basically you can get a 1200 and add a small fortune in slower periphrials to it,and have dongles popping loose half the time,or a box stock a4000/040 you dont have to add 50 things to.
So in conclusion half you people either never owned anything but a 1200 or don't compare specs worth beans

the information is out there plain as day.
Mike