Oooh excitement!
General:1) I'd love to see some checkboxes up on the main menu to define whether or not you want PCS2 to rebuild the BSP cache (but be sure to call it "Collision Data") upon saving, as I think that would be quicker and easier to remember than the Data->Purge option.
2) With the default colours, could the wireframe overlay colour for subobjects be set to bright red or something other than the same white that the wireframe view uses? That way you can tell what you've selected!
3) A 'recent files' list in the file menu
4) Some definable 'quick jump to folder' options in opening/saving, since currently it just remembers the folder you were last in
5) A default save name - currently even if you've opened an existing pof, when you go to save it you will have to type in the name of or select that same pof to give it a name, since that field is blank by default. The number of times I've overwritten the wrong model by mistake cos of that.... :\
6) Might be pretty tricky, but having a centre of rotation for the camera that moves only when the camera is panned. (Panning is Shift + Left Click + drag for anyone who was wondering) Currently if you zoom in and then pan to focus on a subobject, as soon as you rotate the view, you're left staring at empty space or some other random bit of your model, as the view is rotating around the ship's centre.
7) Slowing the panning speed down too would be good!
8) Clearer button icons - since it's always struck me as a bit pointless to try and differentiate movement constraint planes on a cube.

It really needs to be a nice neat ship outline. A ship with a clear front and back, top and bottom so you can instantly tell if the plane you want to activate is the right one. Something even newbs will recognise would be great, like an X-wing or hercules.
9) Buttons to switch to the directional views (including reset) that are currently accessed from the view menu.
10) A "Do you want to save the changes you have made?" message box when you try and close the program.
11) A "Quicksave to PMF" button on the main bar, since PMF is a lot more stable than POF during the saving process. It would save a PMF to a tempoary directory in PCS2's installation folder.
Tree Menu thing on the left:It's very cool and definitely a huge help, but a few tweaks I would love to see:
1) Better memory of its last state, as after any edit of a low level item such as a drag and drop will cause it to reset the area you're working on as well as the position of the vertical scrollbar if you're working on some area down the bottom. For deeper edits such as subobjects or paths this gets to be very frustrating.
2) It would also be cool if it could redraw faster or not completely redraw every time there's a change.
Subobjects:Yeah selecting multiple subobjects to edit at once would be very handy, but if that's not possible:
1) Switching the 'Movement type' and 'Axis' options to be radio buttons would make them a lot faster to use
2) Not sure if it still does, but at some stage PCS2 imported subobject data and attributes based on their subobject number rather than name, so if you reconverted a model and that threw out the order, everything would get soooo mixed up.
3) A few auto-generate data buttons would be very handy such as:
"Turret" which would enter:
$special=subsystem
$fov=180
$name=Turret
and "Radar" which would enter:
$special=subsystem
$fov=360
$name=Radar Dish
$rotate=3
Turrets:DEFINITELY change the "Parent" and "Physical" labels to "Turret Base" and "Turret Arm" respectively!!!
This might be better in the subobjects area or both, but an auto-gen feature to intelligently set up turrets. What I'd imagine it would do:
1) Clear all existing turrets in the turrets list
2) Look through the subobjects list, pick out 'turret' in the subobject names or subobjects that have been given turret subobject properties already.
3) Add the default turret data to those subobjects (not their arms) that need it.
4) In the turrets section, create a turret for each turret subobject it found, and set them up with their arms as well if necessary.
5) Have a guess as to what direction the turret is pointing in based on the parent subobjects position relative to the centre of the model and set that direction as the normal. (Just the basic 6 directions would be fine - I can write a series of rules to follow if needed)
6) Plonk a single firepoint at the origin of the turret or turret arm. If you wanted to be really snazzy you could place it at the extreme of the bounding box (ie, so a turret arm pointing up you'd pick the middle of the highest plane of the bounding box) but its usually safer to just use the origin.
Paths:1) Could we possibly get little floating number labels for each path point of the selected path, and a note reminding users of which end to start at and go to. I keep forgetting! Point 1 is furthest away, point<last> is closest to the final destination/objective.
2) The ability to select a path point by clicking on it.
3) Maybe make a drag and drop control to change the radii of the currently selected path point. Ctrl + Middle Mouse + drag might work best. Towards the points origin would shrink, away would expand.
Eyepoints:It would be good to change the default colour of the selected eyepoint to bright red so it's more easily spotted!