Internal nipples. Internal cable routing. Certain mountain 4-arm chainrings won't mount to certain cranksets, even though BCD is correct.
Integrated headsets aren't too bad. Like most new stuff if you have the right parts and tools, you're OK. Still, I'd be a lot easier if headsets were all one standard. Same goes for bottom brackets, stems and bar diameters, cassette spacing, shifter cable pull ratio, seatpost diameter, front derailleur clamp diameter, derailleur hangers, brake pads (disc and rim), chains, spoke lengths, and basically every part of a bicycle.