Ugh
Interesting questions, which doesn't have a single correct answer. I don't know what would the best solution for you, but I can tell what way has worked for me.
1) Organising test is complex question. The best solution which has worked for me is to organise test based on features. In a product, I have feature x, example user management. All the tests related to that feature are inside of user management folder, example user creation, modification and deletion are separate suites (at least files or can subfolders with files). In this way it's easy to find all the correct test for the feature and it eases the maintenance too. Also it helps me to use Robot Framework __init__ files efficiently.
2) There are many ways to overcome the problem with adding arguments to keywords. One is to use default values for keywords[1], it works nicely for many cases. But because many things are global in Robot Framework, I have been moving to towards extended variable syntax[2], where I pass single object to keywords. It has been useful for me with connect/setup type of issues, where the argument amount may change because environment or version changes.
I don't rely on the execution order of test suites. I do rely on test execution order in a file, but I would like to give up from that dependency too. When I did rely on suite execution order, it did soon become a maintenance nightmare. Example it might feel tempting to run user creation test suite as setup for user deletion. But it turned a maintenance problem, because I could not make changes to a test suite, because changes did randomly broken other suites.
3) The report and log file being too big can happen, although you may encounter other problems before you hit this problem. I think the Robot Framework has more than thousand tests and one can open the report and log files quite easily.
But if this comes a problem one can always post process the outputs[3].
-Tatu
[1] http://robotframework.org/robotframework/latest/RobotFrameworkUserGuide.html#default-values-with-user-keywords
[2] http://robotframework.org/robotframework/latest/RobotFrameworkUserGuide.html#extended-variable-syntax
[3] http://robotframework.org/robotframework/latest/RobotFrameworkUserGuide.html#post-processing-outputs
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