Though I'm using Standard Window since its introduction, I was using it only for my free time projects. I'm using it for professional repo since just a few month.

And... I'm missing 2 right click options : 

- on a branch, "fast-forward merge" : allow to update a local branch with just one click, without the need to do a checkout, pull, then go back to the previous branch

- in the history, "reset..." and "reset advanced..." : there is the ability to add a "reset" icon in the toolbar, but I'm very used to having the action in the contextual menu

Can both of those be added ? 

In previous versions, SmartGit allowed setting the x-bit (execution bit in chmod) via GUI. E.g. in a right-click menu on *.sh files. This menu entry on Windows seems to be missing since a few versions or the condition to display the menu entry is just sporadically true.

I remember a "Set execution bit" command in the context menu.
Is this option dependent on the file type / extension?

That's my current context menu:

Since the default action is the wrong about 50% of the time (start new feature).

There's an option to scroll mouse wheel while [Branch:] input is focused. It will bring items from the dropdown one-by-one

The issue is that it replaces the entered value unrecoverably. Whatever you've written there will be lost and replaced with dropdown item you've scrolled to. For me it is usually an unintended action while pressing the [Add Branch & Checkout] button: I can accidentially trigger mosue wheel and it will do what I didn't want.

Solution: we may cache current value as one of the dropdown items, so when yopu scroll back it is reverted to whatever has been input there (the edited/new value). Thus we'll get an option to have what we had and use the scroll feature.

To avoid accidentally pushing commits to the remote, could you remove the "Push" check box and replace it with a button  called "Commit & Push".

In the standard window, all repositories are opened as new tabs. If we have multiple repositories of multiple groups, we cannot identify easyly which one is of which group.

I would recommend if possible to adopt the "tab group" implemented in multiple browsers. When opening a repository, the new tab would be part of a tab group named after the repository group. 
This tab group could be collapsed or expanded if needed.

When resolving conflicts, I love using the "Base Changes" screen to figure out what each string of commits changed. It would be helpful, however, to see who made those changes and why.

Currently we mark a Repository as favorite 

It would be handy to be able to mark also Repositories' Group and submodule inside parent Repository.

We have some useful command-line arguments.

But smartgit.sh always creates new windows.

Can a new command-line parameter be added, to apply all parameters like --log and --open to an already opened SmartGit instance, if any?

If there are several SmartGits opened, modify any of them.

If there is no SmartGits opened, ignore the new parameter, open new SmartGit.
By the way, it would be great if --anchor-commit argument worked with --open flag too (not --log only), just focusing the commit specified.