As sales to voucher holders were unrestricted only a thousand were left when they went on general sale, and even though those who turned up at Glanford Park were restricted to one ticket they had gone by midday.
Tickets were sold on the black market, as were forged vouchers - leading to harsh criticism of the club.
Wharton promised to listen to the complaints of any ticketless fans who wrote to him explaining how they missed out.
He has now responded by unveiling a fresh loyalty scheme, and proposing structured stages of ticket sales.
He said: "I hope these proposals will now avoid any repetition (of the Leeds fiasco) but I stress that they are still only proposals and the comments of our supporters will be welcomed.
"It is impossible to find a perfect answer but a lot of time and effort has gone into this and it is a purely voluntary scheme."
The new loyalty scheme would replace the existing loyalty card, and if purchased would cost £10 for adults and £5 for children, students and OAPs if bought before the end of August - with the prices doubling if bought after this cut off date.
Under the new proposals season tickets will have priority to purchase up to four tickets for home games, or one for any away game. Loyalty card holders will also have priority for a single ticket for home or away games - with benefit also given to those who signed up before the end of August.
The ill-fated voucher scheme could also been employed, with voucher holders given priority behind season ticket and loyalty card holders.
After the three stages of priority have elapsed tickets will go on unrestricted general sale on a first come first served basis.
Players will be restricted to four for friends and famliy until the unrestricted sale, when they will have first choice on up to four additional tickets.
Wharton insisted that club staff will adhere strictly to the policy, and the increase in office space currently being built will also create improved facilities for selling tickets.
He added: "Every effort will be made to make season ticket holders and loyalty card holders feel appreciated and that Scunthorpe united really is their club."
Initial reaction from Iron fans was positive, with supporters on the Iron-Bru.net message board backing the plans.
Fans with comments on the proposals to make to the club should write to Mr Wharton at:
Steve Wharton
Scunthorpe United Football Club
Glanford Park
Doncaster Road
Scunthorpe
DN15 8TD