Casting my mind back through the cobwebs of time to when the original ST - STFMs were on sale, I think the biggest thing that held it back was the lack of ease in upgrading the memory. When going to purchase a computer in a shop you had to choose between the 520 ST or the 1040 ST in you wanted more memory. If you choose the 520 to save some money to spend on software, and wanted to upgrade the memory later, then you either had to know how to solder or had to pray that your motherboard had a socketed MMU and Shifter chip so that you could use one of the upgrades that plugged in to them. With the Amiga you just had the 500 and if you wanted to upgrade the memory to 1MB you bought a little board, opened a little hatch on the underneath and just plugged it in. You also got a battery backed clock for your trouble.
Second thing I would of liked would be to have a battery backed clock installed in the ST from the start, a simple thing that would cure the annoyance of having to set the clock all the time.
The third thing I would have liked is to have the OS on a cartridge (like the Atari 800 did), so that you could upgrade it easily, and if you found that something did not work with the new OS, just plug in the old OS cartridge.
The final thing I would have liked on my original STFM would have been a socked CPU, so I would not have had to spend all that money getting it socketed so that I could fit in the TOS upgrade board I bought and a CPU+FPU upgrade board (on top of that) that could run at 8 or 25 mhz (which didn't work at that speed because of the low quality half meg of ram I had on the board and could not be bothered to disable). One thing that is strange is why are there so many different motherboard versions of the STFM, adding a space for a blitter but not putting one on the board, moving the memory around, using more or less chips for the TOS.
Now moving on to the STE which I bought a couple of years ago, if it had been able to run at 16mhz like the Mega STE could, then I would have upgraded to that at the time. Instead I bought a Mega drive and then inherited the bosses old Compaq laptop with a 386 running at 25mhz and 12 megs of ram running windows 3.11. (Glad that PC's had finally caught up form the dark days of DOS, but not so happy with fiddling with config.sys and autoexec.bat everytime I wanted to run a game but having to lose the ethernet driver, and the netware driver etc). The laptop originally cost £3,000.00 in 1991 (i think, might have been later).
I also aquired an Amiga 500 and 1200 myself a couple of years ago and I find the workbench OS, which has to load from disk or Hard disk, to be not as easy to use as the GEM desktop and is languising in a box whilst my STE sits under my monitor / tv with the excellent Ultrasatan attached to it. The Amiga 500 has a main expansion port but apart from a hard disk and cdrom drive, nothing much else I can see got released for it, and it did not have a SCSI port on the back of the Amiga itself. The ST ASCI port had not only hard disks and cdrom attachable but also Ataris lazer printer, a PC cpu box and the Transputer CPU/s box attachable and you could have also bought a SCSI ethernet adapter around the time (but I do not know if it would have worked as the ASCI port lacked some of the functions of the SCSI port).
The thing is, I think some people have forgotten about how much things cost back then, memory cost an arm and a leg, powerful CPU's cost the same as a complete STFM, SCSI cost a lot too, and the hard disks were fairly small in capacity. But SCSI was faster than IDE for a long time and was more reliable. When I was looking after a UNISYS mainframe computer which had three packs of 4 x 20 meg SCSI hard disks I only had one hard disk failure. (The mainframe cost £75,000 second hand and the printer attached to it which produced reports cost £26,000, pity they didn't throw in a free Ferrari with the deal)
During the time I was using the ST I really enjoyed the popularity it had, the Atari scene in the UK really changed when Jack Tramiel was running the show. I had a bleak time with the Atari 800 (where I lived) when Warner Comms controlled Atari.
Also remember, alot of mistakes have been made by others as well as Atari. Sega messed up after the Megadrive, Nintendo messed up after the SNES, IBM do not make IBM branded computers anymore, Compaq has been absorbed into HP, TIME, Panrix, Tiny have all gone. Also Acorn who had some fantastic designs for the Archimedes / RISC PCs did not succeed either (I think the abilty to add power to your computer by adding a Slice was a great idea).
Anyway now days Windows PCS wind me up on how long they take to load up to a useable desktop (despite dual core, lots of ram, big fast hard disk). Macs OS X take far less time, but my printers do not work over ethernet.