Minimize/unminimize animations do nothing for the first 100ms or so

Have you checked whether this issue is still present with GNOME Shell 3.25.91?

Yes, it had the same problem when I was testing the 3.25 PPA. And I can see the issue is still in upstream git:
  https://git.gnome.org/browse/gnome-shell/tree/js/ui/windowManager.js#n1191

Status changed to 'Confirmed' because the bug affects multiple users.

Btw it's even worse with time - if you run your computer for 2-3 days those action start taking not 100ms but 1500-3000ms

In theory that should never happen... If a machine is no longer able to provide adequate performance then the animation should be 0-1 frames long instead. But thanks -- that's an interesting observation that probably also needs fixing. Probably with a separate bug.

https://gitlab.gnome.org/GNOME/gnome-shell/-/merge_requests/2066

This bug was fixed in the package gnome-shell - 41.3-1ubuntu1

---------------
gnome-shell (41.3-1ubuntu1) jammy; urgency=medium

  * Merge with debian, containing various upstream fixes:
    - Window size is wrong after exiting full-screen (LP: #1947467)
  * debian/patches: Refresh to support GNOME 41 codebase
  * debian/patches: Remove patch to make overview starting optional
    This can be handled fully by the extensions that need it, so let's
    handle this in dash-to-dock instead that in upstream code
  * Remaining changes with debian:
    - Replace gnome-backgrounds dep with ubuntu-wallpapers and Suggests
      gnome-themes-standard-data, gnome-backgrounds
    - Add some Recommends:
      + ubuntu-session (| gnome-session) to have the ubuntu session available
      + xserver-xorg-legacy
      + yaru-theme-gnome-shell for the default ubuntu theming
      + gnome-remote-desktop to provide remote desktop support by default
    - Moved some Recommends to Suggests:
      + chrome-gnome-shell
    - Update debian/gbp.conf with Ubuntu settings
    - gnome-shell-common.prerm: Remove deprecated ubuntu theme alternative
    - ubuntu/desktop_detect.patch:
      + add caching for desktop detection to avoid querying the current
        desktop env variable as iterate through the list each time. For the
        time of the Shell process, we can expect this env variable to stay
        stable.
    - ubuntu/smarter_alt_tab.patch:
      + quick alt-tab (without showing up the switcher) switch only between
        the last window of the last 2 applications to be focused instead of
        raising all windows of those apps.
    - ubuntu/lightdm-user-switching.patch:
      + Allow user switching when using LightDM.
    - ubuntu/lock_on_suspend.patch
      + Respect Ubuntu's lock-on-suspend setting.
    - ubuntu/background_login.patch
      + Change default background color as we modified the default GDM color
        for our ubuntu session.
    - ubuntu/gdm_alternatives.patch
      + Add support for GDM3 theme alternatives
    - optional-hot-corner.patch
      + enable patch proposed by upstream developer already in package (but
        not in series) to add a settings for optional hot corner activation.
    - main-show-an-error-message-on-gnome-shell-crash.patch,
      global-make-possible-to-set-debug-flags-dynamically.patch,
      main-increase-the-granularity-of-backtraces-in-SHELL_DEBU.patch,
      main-add-backtrace-crashes-all-and-backtrace-all.patch,
      sessionMode-add-support-for-debugFlags-parameter.patch:
      + Improve debug JS tracing for crash reports
    - ubuntu/search-call-XUbuntuCancel-method-on-providers-when-no-dat.patch:
      + stop searches when requested from UI
    - magnifier-Show-cursor-when-magnifier-is-enabled-and-scale.patch:
      + Show monitor scaled cursor when magnifier is enabled
    - ubuntu/layout-Make-starting-in-the-overview-optional.patch:
      + Makes dock replace overview easier
    - ubuntu/layout-Try-to-allocate-before-getting-size-of-tracke.patch:
      + Ensure windows don't get maximized under the panels / dock
    - Break gnome-shell-extension-desktop-icons (<< 19.01.3+git20190814)
  * debian/patches: ...