As far as I know, the master systems, like engeneering, or the "phasers" master system for instance are not showed on the icon. I never place them, they are not targetable and none targetable systems cannot be damaged by enemy fire. I tested this by blasting away at the fwd phaser of my original p81 norway HP in which for some reason I accedently set the fwd phaser array to non-targetable. Despite firing numerous shots, obliterating the hull exactly on the spot it fired from, no damage indicator came up, and the system couldn't be destroyed. I've never personally seen a non-targetable system show up as damaged on the p81 connie or reliant, and I've destroyed both in battle. Since I've never touched them from defauly, and my current abbe hp is a modified FCA, then those icons are off to the side lower right corner, and I've never seen icons show there on either my display, or the damage display/target menu when I am destroying the FCA. At the very least, add a filter switch/checkbox to nix systems listed as "non-targetable" if desired.
Is there a way to set a folder path that it automaticly looks in? 
*auto-load icon? Ie if I load SFPMontana.py then SFPMontana.tga would automaticly pop up if in the same folder with the py? That could be a handy feature.
 
*It may also be helpfull to make the ship background changeable from white to black. Doing a white tmp vessel on a bright white background is annoying to look at. 
*I am messing with the damage right now and the drag is not smooth when holding an icon and moving it around. It's perfectly smooth on the weapon arc display, yet lags to beat hell on dmg.
*the original TDE used a mouse button system for arcs an indicators, where left click selects the charge arc, right click selects the grey arc indicator. That method is more efficient than having to constantly change mode via checkbox below the display. This would result in the nessecity of a dual set of x/y fields needing to be added, obviously, like the old TDE. (icon link makes this somewhat obsolete but sicne the feature needs adjusting, badly in some cases...) One thing that is really annoying is that if I want to place a different indicator on something I can't unless I switch the button. I should only need to click the indicator.
*Fwd and aft indicators are not linking properly (ie missaligned badly)
*Icons revert to original position if you switch to a new property without clicking "apply changes". Throw out this extra step and have the program remember, live, where you've placed and icon. You can save the entire project at any time using the save from the top menu. If you placed an item incorrectly, you simply click and drag it somewhere else, auto-revert isn't nessecary on such a simple process. On the same token, the X,Y position boxes do not update live. Even after "apply changes" they remain at the old values unless you go to another propery and come back.
*Remove the whole mouse click update for weapons arcs. On complex ships, like anything with a dozen or so phasers, eyeballing to simply click and update (similar to the why you place a property in the mpe by clicking and hitting "get position) is more trouble then it's worth. (easier to drag/hover and be done with it) On the damage display it is logical because the damage icon such as a nacelle will be on the nacelle. Click the nacelle, press the button. Again, live update of X/Y as the icon is moved.
*manualy updating of the X/Y has no effect on the damage icon at all. Why is this needed? Multiple torpedo tubes. If I have 4 torpedo tubes on the same side of the ship, I want those little green dots in a nice even line. I am going to want them to all share the same X or Y coordinate, depending if they are a side launch or fwd/aft. Changing this and pressing apply does nothing, the revert back to their old values after I switch properties. Manualy changing this SHOULD have a live effect on the display above.
I reallise this sounds like alot of nagging, but I've HP'd over 300 ships in my time in the BC community, and I can find plenty of reasons to stick with the OLD TDE. In some situations it is easier to use, faster, or allows things to be done yours doesn't. The fact that you don't need to compile or covert icons to BMP, even an improved icon linking wont quite push me to switch. Obviously, however, if you truly wish to make your product superior to the old TDE, I am more than willing to consult on future versions.
Edit: Accedental close saftey block...if change have been made to the display since the last save, a save prompt should appear when attempting to close the program.