The changes are based on feedback at nine public hearings and from thousands of emails, letters and phone calls, the MTA said.
"While our budget deficit forces us to move ahead with most of the cuts, we were able to take a number of the most painful cuts off the table based on what we heard from our customers," said MTA Chairman Jay H. Walder.
The changes reduce the savings achieved by the service cuts from approximately $101 million annually to $93 million, adding $8 million to the approximately $400 million budget shortfall not yet addressed by cuts.
The revised package will be considered by the MTA Board at its meeting on Wednesday.
A related proposal to phase out student MetroCards will be taken up later in the spring.
The proposed service changes are part of a package of actions proposed in December to close a nearly $400 million deficit for 2010. MTA faces an additional shortfall of $378 million has since developed due largely to deterioration of projected payroll tax revenues.