After looking at Martin O'Malley's website and examining his "vision" link, I think I have a pretty good idea of which issues are on O'Malley's main agenda. As you can see, O'Malley has a "15 Goals" link and then 14 other links under that. I thought it was most important/helpful to look at the "15 Goals" link to figure out which issues were the most important. O'Malley's first goal is to "Increase American families' median net worth by $25,000 in 10 years". His second goal is to "Generate 100% of American Electricity with renewable energy by 2050" (Remember this? Skip to 0:45)
Goal number 3 is to "Cut the unemployment rate among young people in half within 3 years." Goal 4 is "Reach full employment for American veterans by 2020. And goal number 5 is "put 11 million new Americans on the pathway to citizenship through comprehensive immigration reform." I think these 5 goals reflect the top 5 "issues" O'Malley and his campaign's agenda. The 14 issues under O'Malley's vision tab are posted alphabetically, but his 15 goals section seem to be ranked in priority. Not only this, but these 5 issues seem to be the issues he talks about the most.
When looking at O'Malley's opposer Hillary Clinton, the first 5 issues listed on her site were 1. Campaign finance reform, Campus Sexual assault, Climate change and energy, College, and Criminal justice reform. Hillary's issues differ from O'Malley's in that her top issues seem to be on social issues, rather than economic (although that is not the case for all of them).
O'Malley and Clinton's agendas are similar in that they both agree to focus on climate change. I think if you look further down on both of their lists, you will find more similarities. However, if I am assuming that the order of these issues represents their priority to the candidate, it seems they do not have a very similar top 5. I think one of the reasons O'Malley has different issues he's focused on would be because he is having to try and differentiate himself from Hillary. He can't have all the same goals and beliefs as his opponents and expect to win because of it. He has to make himself stand out in some way, and I think that's why there is some what of a difference. I think he's doing a good job of that and is succeeded in setting his agenda effectively.