The problem with #1 is that whilst airline A might fly from city A to city B via city C (because it has a hub in city C), airline B might have its hub in city B instead and might have a direct flight. So airline A has to price its flights to city B at similar prices to airline B to get passengers even though it actually costs them more than airline B.
#2 I agree with, having a uniform "this is the price you will pay" displayed based on the trip options you select and your location (to cover any taxes etc you need to pay) will make it easier to compare things. No more adding surcharges after you start the booking process.
As for checked baggage, the way to go is to have a strict size limit for carry-on baggage enforced at the gate (no more bringing massive suitcases as carry-on to avoid the checked baggage fees) where anything bigger than the size limit is required to be gate-checked (which needs to attract a fee higher than it would have cost if you had just checked it in the first place). Doing this will encourage people to pre-purchase checked baggage with their ticket but without penalizing those who genuinely CAN get away with just carry-on (carry-on that meets the size limit)
#5 wont work, a lot of the time the delays aren't due to things the airline can do anything about like weather. No way should the airline be required to compensate passengers for delays beyond their control.