Under Settings -> Customizations -> Customize the System expand the base entity for the charts and then expand the charts node. Select the chart and from More Actions, pick Export Chart. Save the chart and then open in your favorite editor.
For Funnel charts look for the section:
<ChartArea>
<Area3DStyle Enable3D="false" />
</ChartArea>
Change the value to "true"
<ChartArea>
<Area3DStyle Enable3D="true" />
</ChartArea>
Save the file and then back in CRM and under the More Actions menu, pick Import Chart. Browse the to file you just edited and then choose to overwrite the existing file or upload a copy. If you chose the later, provide a new name.
Before
After
The downside is that this change doesn't translate over the the tablet client.
For bar charts look for the section:
<Series ChartType="Bar" IsValueShownAsLabel="False" Color="91, 151, 213" BackSecondaryColor="112, 142, 50" Font="{0}, 9.5px" LabelForeColor="59, 59, 59" CustomProperties="PointWidth=0.75, MaxPixelPointWidth=40">
<SmartLabelStyle Enabled="True" />
</Series>Change it to something like this:
<Series ChartType="Bar" IsValueShownAsLabel="False" Color="149, 189, 66" BackGradientStyle="TopBottom" BackSecondaryColor="112, 142, 50" Font="{0}, 9.5px" LabelForeColor="59, 59, 59" CustomProperties="PointWidth=0.75, MaxPixelPointWidth=40">
<SmartLabelStyle Enabled="True" />
</Series>Before
After
If you still have access to a CRM 2011 environment you can export the charts and use them as a basis for what needs to change.

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