The Motorola 68000 has 16 (somewhat) general-purpose registers of 32 bits each, a generous complement by the standards of its day. I would expect these to take a significant fraction of the die area. (If they didn't, there would be little reason for competing microprocessors like the 8086 to fail to provide something similar.)
Back of the envelope calculation, 16x32x6 (static memory takes six transistors per bit) = 3072 transistors. The 68k is reckoned to have 40k transistors if you don't count microcode, almost 70k if you do. So the memory cells for the registers should take somewhere around 5% of the die; maybe it's closer to 10% if you also take the access circuitry into account?
That is surprisingly small, sufficiently so that it seems like 32 registers could've been provided. (The ARM-1 did exactly that, somewhat later but with similar process technology.) Maybe the instruction encoding space would have been considered a problem. Or maybe the designers were considering use of compiled languages, and noting contemporary compilers were not good at using lots of registers.
Trying to find an annotated die photo, I found this: http://www.easy68k.com/paulrsm/doc/dpbm68k2.htm
Which... doesn't mention the registers at all, nor leave any unaccounted space where they could be.
Is there an error in the annotation? or are the registers part of one of the marked units?