What truly bugged me from the start is clunky to use equipment screen.
Some of us have sooo much from normal and raided equipment that it takes 5+ pages in each section.
I wonder if there a way to make it easier to use.

First idea was the ability to merge the same type and condition items into one.
It would have a small number in the corner of the icon allowing you to see how many are grouped.
If one of the stacked items needs to be removed or sold, simply ungroup the stack to do so.
But maybe its better to change how the base of the equipment screen works to begin with?

Yes the equipment screen could use work. I like your idea of being able to stack like items allowing them to be all installed or uninstalled in one click would be great. You could have an "expand" button on the groups to get to the individual modules. Another way to do this would be to have a weapons tab just for weapons, a tab for combat items like the mechs the combat analyzer and so on, a defense tab, a shield tab. an engines tab for the energy producing items, a relay tab for all the energy charging items, The hull tab works well, then a scanner tab and a cloak tab. Not sure which of these options I would like better but either would make the equipment area work more smoothly.

I cant lie I got the grouping idea from eve online

Personally, Id love to have a large picture of my ship with blue-print style lines pointing to various sections with links such as "weapon systems", "engineering systems", "structural systems", "defensive systems", "sensors" etc... When you click them it would have a pop up that will be split into two. Top would be what all I have equipped and bottom would be my related inventory. I could then select or drag them to the top in order to equip. (from what I understand this is not a flash based app, so the dragging might be an overkill X_x)
Making icons smaller would make it easier if combined with an ability to expand the "info" showing you the large icon and details of item...