Ok, you can now do this with dimple v1.1.4.
In the latest release you are able to assign data to a series instead of the chart if you wish. Therefore you filter the dataset into 2 parts and assign one to each series.
Here's an example of using 2 data sets on different axes. Hopefully it will allow you to achieve what you want:
chart = new dimple.chart(svg);
x = chart.addCategoryAxis("x", "Fruit");
y1 = chart.addMeasureAxis("y", "Value");
y2 = chart.addMeasureAxis("y", "Value");
s1 = chart.addSeries("Year", dimple.plot.bubble, [x, y1]);
s1.data = [
{ "Value" : 100000, "Fruit" : "Grapefruit", "Year" : 2012 },
{ "Value" : 400000, "Fruit" : "Apple", "Year" : 2012 },
{ "Value" : 120000, "Fruit" : "Banana", "Year" : 2012 }
];
s2 = chart.addSeries("Year", dimple.plot.bubble, [x, y2]);
s2.data = [
{ "Value" : 110000, "Fruit" : "Grapefruit", "Year" : 2013 },
{ "Value" : 300000, "Fruit" : "Apple", "Year" : 2013 },
{ "Value" : 140000, "Fruit" : "Banana", "Year" : 2013 }
];
chart.draw();
Here's a working fiddle: http://jsfiddle.net/NCW89/