Every transistor has capacitance associated with the PN junction.........It's what you learn when you go to school.
It can't be eliminated.
It's always there and each switching stage adds more.
Within the microprocessor, there's the "clock" which sets the data rate, the faster the clock, the less delay between inputs and outputs........that's the second source of delays. The software it'sself adds delays.
It's something that you have to live with and understand how it works.
If you look up the PDF datasheet for any typical electronic component, it will usually tell you what the delay is....it's that delay which determines the maximum frequency that any device will run at.
For example a VB921 which is often associated with a megasquirt.
http://www.alldatasheet.com/datasheet-p ... VB921.html
Typically a 20 to 30 microsecond delay, not a lot but that's only in the output stage, it doesn't include anything in earlier stages.
An ignition coil is an inductor and delays are caused by inductors as well as capacitors.....so an ignition coil it'sself will always add to any delay, purely because it's an inductor.