First and foremost - professional surface mounted components for reliability and full moisture proofing of the circuitry.

Once the hardware is good to go - then top of my head and in no particular order, some things you don't see enough of in lower end ECU's.
(And some you never see but would be awesome to have)

• User adjustable load and speed breakpoints for all tables (Fuel/Spark/Boost etc)
• Accurate PWM temperature based idle control.
• Closed loop boost control
• Adaptation functionality
• Auto tune
• Good knock control
• Thermal control of boost and fuel tables via EGT input
• Live trace adjustments
• Replayable trace history
• A trace you can actually see on the screen in daylight (not black and bloody green)
• Auto table rescaling after inputting new fuel pressure and/or injector size
• Fan output control
• Vehicle speed input and output control
• Fuel table targets in AFR with correct modelling to achieve the results
• Option to change from speed density to Alpha N.

Would be nice to see an option to base the firmware on a modern torque model with accurate axle data to give it correct gear knowledge and thus spark, boost and fuel tables for every gear instead of one generic table.