Flowgorithm is an amazing program that introduces pupils to the computational thinking in algorithms. Drag and drop flowchart creation which can actually run with input and output, has a debugging mode, variables watch and it can also generate code in many programming languages, e.g. Python, which is straight copy+paste to IDLE to run (just watch out for casting, have to use ToString(i) when printing out output. It will also do pseudocode. The official site is http://www.flowgorithm.org/.
Oh, and it is also free and has a portable version that can run off a USB stick or network folder with some permissions set. (Portable version is here).
The problems? Yes, there are some compromises.
About the last limitation - as it's a single file, it is possible now to run it on a Mac/Linux under Wine (Windows Emulator) which is free. See the instructions for setting up a Windows-only game in High Sierra but the same steps apply to Flowgorithm here.