I suggest an additional view mode, where two thoughts are opposed to each other:

TB, compare mode.png 
Visualisation of commonalities of and differences between two thoughts: which parent/jump/child thoughts are shared by two given thoughts, and which are related to only one of these two thoughts?

Switch from any view (normal, outline, etc.) to "Comparison".
The active thought of the view before becomes "thought A", "thought B" could be same thought as well.
Parent, jump and children thoughts of "thought A" and "thought B" are displayed in between, like shown above; each of these three groups can be scrolled up/down separately.

By default, "thought A" is THE active thought; so, if you search/select another thought X, this thought X becomes the new "thought A".
With the cursor keys, you can navigate the current thought indicator (green circle) to any thought you want; the notes/attachment view should show the data related to this, current thought.
If you press Enter, the current thought becomes the new "thought A" (for the current thought being on the left of the screen), or "thought B" (right of the screen). If you press e.g. Ctrl-Enter, a thought on the left part of the screen becomes the new "thought B" (analog for right part/"thought A").


OSX 10.13 
iMac (Retina 5K, 27-inch, Late 2015)
3.3 GHz Intel Core i5
32 GB 1867 MHz DDR3
thanks for the suggestion I will write it up.
Here's a version for multiple thoughts comparison, just to break the limitation onto only two thoughts to compare:


Additional thoughts (from selection list, or search field) are added to the list on the left side, as well as to that on top.
Names of thoughts on top are rotated counter-clock wise bis 90° [without this rotation, this view is not -imho- that pretty ...].
You can scroll the thoughts lists on left side and on top.
Dots indicate link information as we know (just a circle: single connection; filled light blue circle: multiple connection), additional: filled dark blue circle: identify of thought.s
When a circle is selected, the link (= two lines) is highlighted, and the corresponding thoughts show frames and relation dots; in example above: "thought 4" is a jump thought of "thought 3". [I know, it's a bit irritating - the circle on "thought 3" is in a relative position to the thought's name where it would indicate a parent thought link...].
Thoughts can be removed from the thoughts list on the left side, and may remain in the list on top, and vice verse; sample above: "thought 5", "thought 7"
In sample above, "thought 1" has a relation to a thought on top, which is not visible at the moment.
A link can be modified, or deleted; in later case, only the two lines are removed, the unlinked thoughts remain visible.
A new link can be drawn between any pair of two visible thoughts; it's graphical representation is added to the view according to the ideas above.

One can easily enhance the link handling by showing the link properties either on hover over, or selection of a single link dot.


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