It doesn’t appear that you can label a particular THT pad as “multilayer” and then assign it with its own independent color.
it is a strange attitude to add a feature, but not keeping previous versatility IMO
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Just my 2cents: I encourage developers to do “breaking” changes from time to time to introduce worthful features. Too often, projects are too afraid of deviating from existing workflows which stalls development and useful features! Keeping everything in a SW product resutls in software that is not only extremely hard to maintain but also “eats” a lot of dev time that can be used more appropriately for the better good of “most” of the people.
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for the better good of “most” of the people
top of the post is the better good
this is the worst sentence of these days IMO
I’m not so sure.
The only function deleted is the pad color. If the pad color was still allowed to be user set, and all layers were set to the same color (as in previous versions), the ability to change shapes in different layers would result in the layer with the largest pad always showing on every layer.
The only way to see the pad shape on the layer worked on would be to switch off all the other layers. This would need to be done possibly with most tracks being laid.
To overcome the need to continually turn layers on and off, you would need to assign different colors for pads for each layer. You would then have to familiarize not only different layer colors, but also different pad colors. This would start getting messy with more than a two layer board.
Choosing the same color for pads and tracks on each layer seems like an easy to remember system to me. This is the way SMD on Kicad has worked forever.
I suppose the biggest change needed is for those who use THT to retrain the brain and eyes from yellow colored pads to SMD colored pads.
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Well then let´s keep aside the phrasing or wording. The first days I used Kicad (and that is not long ago, I just started using it as of V7) I wondered a lot about some design decisions of the devs. But just going a bit deeper and using more features and shortcuts I learned that obviously many of them led to a (what I think) is a tool with a rather good user experience.
Back to the color “feature” you don´t like: I like it because It makes every board that is a bis more involved than simple 2 layr boards easier to handle (visually). A lot of tools I used before had some similar features. I am 100% sure there will be future features and design decisions that I will find bad and which will “slow” my usual workflows - until I look at them and learn how to use them for my advantage.
A software, that does not allow the mindset to do breaking changes sometimes without carrying over all the possible options fom the past, is dead IMO
Back to the color “feature” you don´t like
Who told you that?
What I said is simply what I wrote:
it is a strange attitude to add a feature, but not keeping previous versatility IMO
Right, I got that wrong. No offense meant, though 
Only if you think of the previous behavior as “versatility” rather than “the way it was because nobody thought ahead to the desire to have different via sizes on different layers”
just point of view …
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In AD, if the pads (vias) in all layers have the same geometric shapes, then the color is defined by the “Multilayer” layer. Something like the old KiCad. If the pads (vias) have different geometric shapes in the layers, then the color of the geometric shape is taken from the layer color, as it is now permanently in 9.0.0 RC1.
I think it’s a good solution, because I think that multi-shaped THT pads and vias have a very small representation in the entire PCB design.
Please try to think about it.
We have thought about it. The current consensus is that drawing vias differently depending on whether or not they have different shapes is not as good because it means that vias don’t have a consistent look.
So I’m really sorry that you made this decision. I already switched to 8.99 halfway through the year and this change surprised me at the end of September. I thought it would eventually be incorporated into the final version with some choice. Now I’m frustrated. I don’t know what I’m going to do.
Unusual pad stacks are pretty common in industry, due to the use of flexible PCBs. I first came across small PCBs bonded to the kapton flexi in the mid 80s, so 40 years ago.
I’m not describing here that unusual pad stacks are not used or that PCB Layout should not support them. I’m describing here how these unusual pad stacks are displayed in PCB Layout.