Segmented memory made address calculation more complex, but you have to be very careful setting any register before accessing memory on any cpu.
MOVE.W 6(A6), D0
If you don't set a6 correctly on 68000, it will fail as badly as not setting the ds/es segment correctly on 8086.
Your lecturers quote sounds like hyperbole. The 8086 came out in 1978, the 68000 came out in 1979. There weren't any microprocessors ten years prior to that. Mini computers and main frames were still using segmented memory then. I'd be interested in what two years he thinks it was set back from and to and why.
The big problem wasn't even with assembler - as you point out, one more register to set isn't a huge deal when you're already directly working with registers all the time. The big problem was that it did awful things to higher-level languages - most 8086 compilers have distinct memory models you have to select based on whether you want more than 64KB for code, data, stack, or any combination thereof, and have distinct types for near (same-segment, 16-bit) or far (different-segment, 32-bit) pointers - which plays merry hell with C, where pointers and pointer manipulation are a way of life. They also frequently didn't allow arrays larger than 64KB (not a big deal in C, where arrays are just a special case of pointer and you can just use far pointer arithmetic almost interchangeably, albeit at a speed penalty, but a much bigger problem in less flexible languages.) And thanks to the incorporation of this kind of thing into the Windows API, programmers were stuck dealing with it even when the 386 had made it theoretically obsolete - it wasn't until Windows 95 that the stink of segmented addressing was finally washed off.
Also, some minicomputers and mainframes did use segmented memory, but most of them weren't designed that way from the ground up the way the 8086 was (the PDP-11, for example, originally only had a 16-bit address bus, and wasn't provided with an MMU until later - same goes for the TI-990.) They're kludgy because that functionality was actually a kludge; the 8086 was weird and balky right from day one.