When comparing GitHub Desktop vs GitKraken Client, the Slant community recommends GitKraken Client for most people. In the question“What are the best Git clients for Windows?” GitKraken Client is ranked 3rd while GitHub Desktop is ranked 17th. The most important reason people chose GitKraken Client is:
It's modern and beautiful, it looks clean and refined. It's simple: the most used features (pull, push, branch, stash, commit) are accessible in one click, and are the only buttons. The other features aren't in complicated menus nor in hundreds of buttons, but rather displayed when you right-click on something. It gives more space to the commits, i.e. the most important things. In fact, you can collapse or reduce the other menus/windows. It displays the current path (project, branch) on an horizontal (clickable) bar at the top. It's just a matter of taste but I prefer this to the traditional "tree" view. It has undo and redo buttons on the main window. It supports some drag-and-drop gestures (for example: drag-and-droping the local branch to the remote one pushes it).
Specs
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Pros
Pro Great GitHub integration
This is the official GitHub desktop client built by the GitHub team.
Pro Simple, streamlined GUI
GitHub Desktop uses an extremely simplistic two-panel view. It's not capable of complex historical visualisations like other GUIs, but it is very easy to use (especially for git novices).
Pro Supports pull requests
In addition to being able to seamlessly and easily integrate with all of GitHub's features, it also supports forking and submitting pull requests on any open source project hosted on GitHub.
Pro Beautiful user interface
It's modern and beautiful, it looks clean and refined.
It's simple: the most used features (pull, push, branch, stash, commit) are accessible in one click, and are the only buttons. The other features aren't in complicated menus nor in hundreds of buttons, but rather displayed when you right-click on something.
It gives more space to the commits, i.e. the most important things. In fact, you can collapse or reduce the other menus/windows.
It displays the current path (project, branch) on an horizontal (clickable) bar at the top. It's just a matter of taste but I prefer this to the traditional "tree" view.
It has undo and redo buttons on the main window.
It supports some drag-and-drop gestures (for example: drag-and-droping the local branch to the remote one pushes it).
Pro Extremely easy to use
A lot of care has gone into trying to make GitKraken as easy and intuitive as possible and it show. Every action is quick and painless with no more user interaction than necessary. For example, switching to another branch is as easy as a double-click on the sidebar.

Pro Cross-platform
Built on top of Electron, so it runs on Linux, Mac, and Windows.
Pro Offers a simple way of undoing mistakes
GitKraken has simple undo/redo buttons that work the same way you'd expect in any other software.
Pro Some of the best integration with hosted version control services
GitKraken can be connected to Github, Gitlab, or Bitbucket accounts through OAuth. From that point onward most if not all actions that are related to these services can be done inside GitKraken. Things like: cloning or forking a repository, adding a remote, pushing to a remote repository hosted on these services can be done inside the app.
You can even manage pull requests inside GitKraken for example. All pull requests for a certain branch for example are shown on that branch's graph.
Pro Free version available
There are both pro and free versions available. The free version is pretty complete feature-wise for day-to-day operations.
Pro Under constant improvement
A quick glance at GitKraken's release notes shows how frequently it's updated. Updates are released on a 2-4 week cycle and each one brings new features and bug fixes.
Pro GitFlow support out of the box
Supports GitFlow out of the box.
Pro Has a FuzzyFinder
GitKraken has a fuzzy finder to switch between repos/files.
Pro Perfect for beginner developers
GitKraken is easy to use and is brilliant for the beginner developers.
Pro Has a dark theme
No more eyestrain staring at white screens - GitKraken has a lovely dark theme.
Pro Good keyboard shortcuts
Cons
Con Limited
Can't handle complex tasks. The Help Manual advises to use command-line Git instead.
Con Does not support multiple Remotes for a repo
Only allowed to assign one URL as remote. To manage/sync/fetch other remotes, use command-line Git instead.
Con Overly Simplified UI
UI that is designed not to support the needs of power and enterprise users. Management of more than five repos is next to impossible.
Con Buggy
Poster child for authors' programming ideology (FRP), likely the cause for the odd quirks and bugs it has.

Con Not free/libre
This application is proprietary, and thus cannot be modified or freely distributed.
Con No Linux support
There's no Linux version of this client.
Con Non-GitHub repositories are not fully supported
Since this is mainly a GitHub client, other repositories are not fully supported and with as many features and setting up a repo hosted anywhere else but GitHub is troublesome.
Con No longer free for use with private repos
You can use GitKraken for free if you're working on a public hosted repo, but you can no longer work on a private hosted one without paying.
Con Slow
Can take between 2 and 5 seconds to load a repository, if not crashing while loading
Con Must log into GitKraken servers to use the free version
All functionality is disabled unless you register for a free account and remain logged in.
There is the $99/user/yr Enterprise option. It allows you to deploy a Linux License Server in an air-gapped/offline environment.
Con Has memory-related issues
Like most Electron apps, GitKraken has some memory-related issues. For starter, it requires more memory for an action than an equivalent non-Electron application. Although this should not be a problem most of the time for people who use machines with lots of RAM (after all, RAM is pretty cheap nowadays), it can have some issues when opening large repositories and there have been cases where GitKraken failed to open very large repositories or started lagging once they were opened.

Con Not open source
It is gratis (no cost) but is not open source. The community cannot fix problems in it, audit it for security, or trust it in general.
Con Not free for commercial use
The free version of GitKraken cannot be used in commercial projects.
Con Crashes once in a while
Under specific circumstances, like resetting 5000+ changes, the GUI will crash.
Con Has annoying popup reminders that ask you to upgrade to the Pro version
Understandable, since nobody is entitled to use work done by others for free, but annoying nonetheless.
Con Amending merge output is a pro feature
In most cases of Merge Conflicts, users are stuck with auto-merge or manually resolving it by hand. This is because in the Free Tier, users can only (1) Keep File (ver 1), (2) Keep File (ver 2), (3) Auto-merge, or (4) Use External Merge Tool.
In addition, using External Merge Tools is very limited because GitKraken (all tiers) restricts External Merge Tools to only those it managed to Auto-detect. It also does not support custom arguments for the External Tools.
Modifying the merge output directly, or Selecting lines to keep/discard, is a Paid Feature.
Con Can be confusing
Con No real commitement to Linux support
Infinite loop on Fedora 28, no debug feature or stacktrace available, no clear dependencies listing.... No real support on Linux.
Con Ugly, looks like a web app
