- Edited
Bugs or features?
Just updated to 3.6.46 today.
Are these features ore bugs?
Left - creating new bone after selecting one bone (torso) and arm asset. Edges that touch asset canvas are invisible. Pretty sure that's a bug.
Right - only selected anchors weights circles are shown (there were smaller semi-transparent ones on unselected ones before)
It's hard for me to believe it passed beta like this (at least first thing), so I'm probably back to updating only when new version is out there for few days at least.
Also, that happened to me also in prev version:
Am I missing some button? The thing under hierarchy disappeared... You know, the part with options for selected elements like coloring, editing mesh, editing constraints etc. It reappears after restarting. How did I close it? 
Hello jamqdlaty,
About your first problem that you mentioned in the "Left" paragraph, could you please add some details?
- what is happening wrong?
- what did you expect to happen?
- how (which exact steps) did you make it happen? (e.g. from when you opened your file, what tools did you use, did you flag some particular options?)
The second "Right" bug you're describing is a feature. When you have the "selected" option checked, it will only show some of the pies.
However, considering you have a path selected, I think you're seeing the pies if the path instead of the mesh, if you think you're seeing too few pies.
Regarding your last problem, my guess is you probably have a filter on bones in your tree, remove it to make images selectable again. (or please post a wider screenshot to understand better what is going on)
First (left) I expected this (the fat lines I added) 
. The edges of arm assets that touch file edges are invisible when creating new bone and they should be visible. If the asset had no alpha channel (whole file filled), I wouldn't see the selection at all
2nd (right), then I think it's a bug. Whether it's checked or not, I don't see unselected vertices weights.
It was something like this before (photoshopped):
When weights tool is ON but no verticle is selected I can see the smal lcircles, but when I select any verticle, the other circles disappear.
For the last problem, I don't know when it occured. 
But I'm sure the filter was not on, I tried all the things in header of hierarchy panel. It may look like it was on, but back then I had no assets under these bones. It didn't appear even when I selected bones. Anyway I think i doesn't disappear even when the filter is on, it just shows bone options instead of attachment.
Thank you for further explaining your problems. Unfortunately, we can't solve problems if we can't reproduce them, but if you can send your project to contact@esotericsoftware.com (including images) and mentioning this topic, I can have a look at the project and try to understand what could be wrong.
1) If I understand correctly, you have a mesh which does not have translucency at the edges, like this: Image removed due to the lack of support for HTTPS. | Show Anyway Image removed due to the lack of support for HTTPS. | Show Anyway
Spine has never been able to edge highlight meshes like this, instead you only get hull lines on hover:
I see the hull lines when using the Create tool and holding ctrl (cmd on Mac). Is there some situation where you don't see the lines? If so, we'd like to fix it.
2) We changed the weight pies purposefully. When some vertices are selected, unselected vertices change to gray dots rather than small pies. The reason was to reduce clutter when adjusting weights. If people hate it, we can consider going back to showing small pies. We made a number of other small improvements when adjusting weights.
3) I've never seen the properties at the bottom of the tree not appear. They should be there if you have something selected in the tree. Note if you selected 2 different kinds of objects, eg a slot and a bone, then the properties don't appear.
1) Sounds like it was like that forever I guess, maybe I didn't have assets that touch edges so much before.
2) I think the unselected weights pies were a bit too big before, too similar to selected ones, but at least I had some overall view on all mesh weights, seems weird if I can't see other (especially near) vertices while adjusting weights of one.
3) The bug just appeared and I took a screenshot as soon as I noticed.
I can select whatever I want, bones, paths, attachments, but the bottom panel with options is gone till I reset. It's possible that I switched monitors before that happened(I mean clicked some window on other monitor). As you see I had mesh selected with translate tool.
7 days later
Sorry for the delay.
2) Here's how it used to look: Image removed due to the lack of support for HTTPS. | Show Anyway Image removed due to the lack of support for HTTPS. | Show Anyway Image removed due to the lack of support for HTTPS. | Show Anyway Image removed due to the lack of support for HTTPS. | Show Anyway Image removed due to the lack of support for HTTPS. | Show Anyway
I don't think the little, dim pies are very useful, since you can barely make them out. If we don't dim them then it's hard to tell what you have selected:
If we highlight the selected pies, it looks bad:
That's why we ended up hiding unselected pies:
If you need a better view of the weights, enabling the overlay can help a lot:
3) We've never seen the tree properties fail to appear! Do you have any idea what actions you were taking leading up to that happening?
a month later
Sorry for late answer. I'm not sure what caused the properties to disappear. In current projects that doesn't happen. I don't use paths in these, maybe it was somehow related to path constraints.
I'm having a really hard time with the weights circle not showing on unselected... No chance we could choose that in settings? :< What's wrong with the dim circles? Did people complain about it? I had no problems at all distinguishing selected from unselected and now I have to unselect or select everything to see it it looks right, I don't really like the gradientish thing. If I'm editing weight on some vertex by hand I want to see the weights on neighbouring vertices or on vertices that are on the other side (when I do something symmetrical) - I think it makes sense... For me the change is really bad, I hate it.