I think ultimately it's like all PCs builds - what do you want to do with it?
I built a pair of PCs for my kids, for homework, light web-browsing, light gameplay, and that's it period.
I got "budget" ASUS motherboards, Haswell dual-core processors, 8gb RAM and SSDs, and no optical drives in each one. My system OTOH has better "stuff" because I'm a PC gamer/power user.
Different needs, you see. In this context you might say I gave them a pair of 030 A1200s with 4mb Fast and 250mb hard drives in the desktop case because that's all they need.
So if you really see yourself needing that much "stuff" for high-end (for the Amiga) gaming, like playing Quake 1 and 2 (and possibly 3 if you manage to pick up a BPPC), lightwave renders/animation, photoshop through mac emulation or ImageFX, and so on, then the towerized A1200 is the way to go.
If, however, you're after a moderately snappier vintage gaming + modern-ish gaming arrangement plus want the ability to emulate a vintage mac with a reasonable amount of speed, then stick with an A1200 + accelerator + fast RAM. For ease-of-file-transfer get either a network connector or (IMO, the better solution) a USB card and if you need tcp/ip, a network dongle for it.
I'm not a fan of wedge/desktop cases but I think if you want the latter that's your best bet, just stick with one of those...
