Hindsight makes us all visionaries, and who would have thought that many of us would still be using the same hardware 20+ years later, heavily upgraded, heaving at the seams, traces boiling from the heat dissipation of the increased bus frequencies pushed to the limit...
...but here's my 3:
1) Self-destruction batteries soldered onboard in sensitive areas (A4000 - adjacent to ram sockets; A3000 - middle of the fricking board; A500+... well, need I say more)
2) Lack of a user-files area by default on hard-drive OS installations. Software developers invariably used progfile: as the default save-to location. (Now try backing up all your documents from Maple V, Multiplot, Wordworth, Equation editor, Turbocalc, etc)
3) Lack of a ability to use A1200 processor upgrades with the A3/4000, even in a fallback 32-bit memory / ZorroII mode.