The Methodist Church recognizes the good deeds of the people as reflecting the strength of their faith, focuses on 'deeds not creeds' and it's not "salvation by faith alone" or "salvation by grace" alone. The Presbyterian Church believes in justification only by grace and says that the 'predestined elect' is the only thing that will lead to heaven. In other words, Presbyterians say that there is nothing you can do, whether good deeds or even pure faith, which will save you - only the Elect who are chosen by God for reasons known only to Him. Presbyterians are Calvinist, which is different than a lot of Christian denominations. Methodism, on the other hand, holds that individuals choose salvation out of free will, and not just the grace of god. In other words, Methodists think we have to pursue holiness and salvation, Presbyterians think that we are predestined to salvation or not regardless of what we think or do.
You'll find that there are always important doctrinal reasons for differences in denominations. They are significant. If they weren't, denominations would not have broken off.