Welcome 
I’ll only answer this as I’m not competent in the other fields. I speak about the smooth transition later in my post.
In terms of customization, you can edit the CSS from an in-built editor, as well as add Javascript and use Discourse-specific JS API. Visually speaking, if you don’t like something, just hide or change it.
The official theme guide is here, Beginner's guide to developing Discourse Themes.
It may not be completely up-to-date as we’re currently upgrading some JS stuff on the long run.
About 100% of the themes, theme components and plugins published here are open source, so you can always have a look at their code to build your own solutions.
A theme is basically a skin with or without added features.
A theme component usually adds features.
A plugin adds more in-depth server-side features.
For my own communities, I try using only official customizations or others from trusted and well-established authors or companies like pavilion. And also personal ones, of course, as I can maintain them myself.
Themes and theme-components can be added and removed at runtime, while installing and uninstalling a plugin needs a command-line app rebuild (10-15 min downtime).
As for a smooth transition for a community that would alleviate user confusion or angriness, that is sometimes tricky. Obviously, a 100% happiness score is close to impossible.
Plus, some communities are definitively more conservative or louder than others and will react accordingly.
From a user perspective, I’d say the most recurrent criticisms that have been made are:
-
No more pagination
It’s replaced with an interactive timeline. Both have their pros and cons. I’ve occasionally heard people not able to adjust to this change.
My own experience from 3 migrations of small and mid-sized forums is that no one in my communities had a negative experience with the timeline thing. -
The interface is complicated
The interface has more elements than in the past, as features were added over time. The notification menu has grown larger, the sidebar was introduced, and a chat feature was added (which may not be needed if you have a Discord server).
We’re very aware of the complexity of the interface, and we’d definitely like to have more streamlined parts.
There’s definitively a learning curve with Discourse. While being a forum having the same features as any other forum software (post topics, post replies/PMs, that’s it…), it diverges from here in terms of interface and added features. I’d say most people have no particular issue with that, but this forum’s community might be biased as most people here know Discourse.
When you’re used to the interface, you don’t see noise anymore and focus on the features you actually use, but I understand that’s not exactly your concern here as you focus on the migration/transition.
There are two in-built tools that helps people understand the interface and features.
-
@discobot. It’s an interactive bot user that we can interact with, and it teaches us how to use some discussion features.
-
New user tips. When you register, tooltips will appear in the interface to explain different parts. You can disable it at any time from any tooltip and opt-in again from your user preferences.
From an admin perspective, it would be:
- There are too many settings
Yes, there are many options in Discourse. Carefully configuring the forum will take hours and probably need adjustments until satisfied. The good thing is that when it’s done, you rarely go back to tweaking the settings.
We know many settings can be intimidating and sometimes make finding something difficult. There’s room for improvement.
Finally, you can use the user sandbox at try.discourse.org.
There’s no admin sandbox. When I want to experiment with things at an admin level, I usually set up a low-specs Hetzner server (billed per hour) on which I install Discourse for a few hours or days.