I am not saying you should move the HTML to a plugin, only the data-prep.

Looking at your example, I would return a your data already sorted and have everything in arrays of objects. Loop through your arrays and your data will be easier to work with in TT. Example;

[% USE MyPlugin;
   classifications = MyPlugin.classifications( data ); 
%]

[% FOREACH year = classifications %]
    <tr><td colspan=x>Year [% year.no %]</td></tr>

    [% FOREACH class = year.classes %]
        <tr><td>spacer</td><td colspan=x-1>Class [% class %]</td></tr>

        [% FOREACH sub_class = class.sub_classes %]
            <tr><td colspan=2>spacer</td><td colspan=x-2>Sub-Class [% 
+sub_class %]</td></tr>
            <tr>

            [% FOREACH element = sub_class.elements %]
                <td>[% element %]</td>

            [% END %]
        [% END %]
    [% END %]
[% END %]
[download]

As you can see this is a lot cleaner than what you are doing. You can get away with not using objects by just setting a variable which is reference to the nested hash. You should really avoid having to type all this to get the data you want.

FOREACH element IN data.$year.$class.$sub-class.keys.sort
[download]