A new report by Transport for the North says there "may be a case" to introduce a German-style zonal ticketing system where fares are uniform across the North to replace the existing point-to-point structure of different fares for every route.
Its Long Term Rail Fares and Ticketing Delivery Plan for the North comes as increases to rail fares come into force today, meaning the average journey will cost 2.7 per cent more than last year.
A campaign group described the rises to hit Yorkshire commuters as "unjustified" given the poor performance in recent months of the region's two main operators, Northern and TransPennine Express.
Some long-distance commuters saw the annual cost of getting to work increase by more than £100 today despite fewer than two-thirds of trains being on time last year. The price of a 12-month season ticket between Leeds and Selby rose from £1,608 to £1,652.
The average rise for trains run by Northern was 2.5 per cent, while CrossCountry raised prices by an average of 2.8 per cent and London North Eastern Railway by 1.2 per cent. TransPennine Express did not provide an average figure.
Fewer than half of passengers are satisfied with the value for money of train tickets, according to the latest survey by watchdog Transport Focus.
But according to Transport for the North, which will be discussing rail performance next week at a meeting attended by Transport Secretary Grant Shapps, the wide range of products, fares and restrictions on tickets are also off-putting for passengers.
Its report said: "This can make it challenging for passengers to have confidence that the products they choose to purchase are providing them with best value for money for their travel requirements.
"Ultimately, the rail fares offer is a key driver of perceived value for money. The investment in services, rolling stock and station facilities currently being delivered across the North of England will help to raise perceptions of the quality of service on offer.
"However, these gains could be undermined if passengers continue to encounter complexities and perceived unfairness when they consider and purchase their products."
Northern and TransPennine are both investing heavily in new rolling stock and major infrastructure projects including the £2.9bn Trans-pennine Route Upgrade and Northern Powerhouse Rail are promised for the North.
Among the problems with the current system, according to the report, is that the disparity in choice available for tickets across the North "creates an inconsistent experience for travel" and variation in prices create a sense of unfairness for passengers.
The complexity of the system is thought to undermine the vision transport bosses have for the North as a single functional economic area in which people can easily travel to different areas to get to work.
The report suggests an alternative could be found in the Ruhr region of Germany, which covers a number of cities, suburbs and more rural areas. The area is divided into zones and the fare structure has four tariff levels depending on how many zones a journey covers.
This system "allows a simple pricing structure to be applied across a multi-centred area with a reasonable association with distance travelled", according to TfN.
Creating such a structure could make the system more challenging, bosses admit, but they hope the introduction of a pan-northern smart ticketing system would make it easier to negotiate.
The fares increases which come into force today were described by TSSA General Secretary Manuel Cortes as "a slap in the face" for millions of commuters.
Judith Blake, Leader of Leeds City Council and West Yorkshire Combined Authority Transport Lead, said: “Higher fares are never a good way to start the year but rail passengers will find those taking effect this month particularly galling given the ongoing delays and cancellations which are severely disrupting journeys across the North of England."
The West and North Yorkshire Branch of Campaign for Better Transport described the rises, based on July's RPI inflation figure, of 2.8 per cent, as unjustified because of the recent chaos and disruption for the region's passengers.
A spokesman said: "Customers have been subject to abysmal standards of performance over the past year with cancelled, delayed and short formation trains causing time wasting, inconvenience and perpetuating overcrowding.
"The rail industry has a cheek to use its monopolist power to jack up prices. Increased revenue should be achieved by attracting patronage, not deterring it by fare hikes."
Network Rail data shows only 65 per cent of trains arrived at their scheduled station stops within one minute of the timetable in the 12 months to December 7.
South Western Railway passengers suffered from strike action throughout December, while there was major disruption to Northern, TransPennine Express and West Midlands Trains services during much of 2019.
Before Christmas, Northern and TransPennine were told by northern transport bosses that passengers are paying the price for their failures after a new timetable led to widespread disruption and cancellations.
Today's increase in around 45 per cent of fares, including season tickets, is regulated by the UK, Scottish and Welsh governments. This is predominantly capped at July's RPI inflation figure, which was 2.8 per cent.
The Campaign for Better Transport described RPI as a "discredited and obsolete statistic which should no longer be used".
It urged governments to base regulated fare rises on the more commonly used CPI measure of inflation, which was 2.1 per cent in July. Other fare rises are decided by train companies.
Robert Nisbet, director of nations and regions for industry body the Rail Delivery Group, said: "We know that no-one wants to pay more to travel, and rail companies have, for the third year in a row, held average fare increases below inflation while continuing to deliver investment in new trains and extra services that will improve journeys for customers.
"In 2020, we will work together to run 1,000 extra services a week and roll out 1,000 more train carriages as we replace half the country's train carriages.
"We will also continue to push for changes to regulations that would make rail fares match how people work today and tackle crowding on the busiest long-distance routes."
The Department for Transport is expected to publish a white paper based on the findings of the Rail Review in the coming weeks.