Rothnic,
I can't comment much at the moment, but I want to give you what I can.
Lining up ports, destributing them, etc. Basically treat them just like any other element on the diagram, except they are confined to the edge of an element. If you have two part properties on an IBD, both with ports, and a connector. You would want to select each port and the connector at the same time, then align centers. So the connector and ports would be centered.
Non-resizeable diagram frames. I mean when you drag and drop a diagram from the project browser onto a diagram and select "Diagram Frame". For example, if you wanted to have an overview diagram that has large thumbnails of each diagram instead of just a link.
Connectors tied to IBDs. This one I put into a couple long posts with examples and verified 3 other similar modeling tools that do not behave this way. I think it is because this is more a UML focused tool. With SysML, you may design System, with Subsystem 1 and Subsystem 2. If you created an IBD for Subsystem 1, you would use the connectors between the part properties/ports. If I included Subsystem 1 in a special context called "Subsystem 1 Testing Environment", then showed the structural elements of Subsystem 1 within the Testing Environment IBD the connectors would not exist in that context. With SysML, if you wanted to change the internal connections, you would define a specialized version of Subsystem 1 (Subsystem 1 for Testing) and define the alternative connectivity.
http://www.sparxsystems.com/cgi-bin/yabb/YaBB.cgi?num=1374248326 A sample model file and screenshots
http://www.sparxsystems.com/cgi-bin/yabb/YaBB.cgi?num=1382661152/2#2 A follow up, but still don't think this is understood.
Visual Diff: Wow, thanks. Somehow missed this. Scoured the baseline compare of a package looking for something related to "diagram". The toolbar, compare options, right click menu just say compare to baseline. Seems like more intuitive behavior might be to show the full visual diff by default when double clicking on a diagram icon, below or above the diagram properties. Then allow to deselect as needed. Now I need to look into whether I can script exporting these diff diagrams out....