I agree whit point 3 +1 from meI've made my displeasure with engineers pretty well known. However...
1. No one is forcing you to play. So not torture
2. Your proposal is actually worse than the current system. 100 million for rank 5? That is a 12-15 hour grind. Not to mention most players don't even own a ship worth 100 million. And I speak as someone with total assets of 1 Billion.
3. A much more fair way would be to base the cost on the original part cost. After all it is cheaper to modify a Ford than a Ferrari.
That way the guys flying vipers can afford engineer mods too.