Here are some thoughts:
1 - 4: These are all not currently within the paradigm of Tableau Prep. One highly requested feature is moving nodes (steps): https://community.tableau.com/ideas/8964 and you might want to add your support to it and additionally create new ideas for grouping or adjusting connecting lines.
5. This one is possible, though not as seamless as it should be, in my opinion. There is an idea for joining (and I would hope union too) based on position: https://community.tableau.com/ideas/8793. A possible work-around is to adjust the Input Step for each sheet/file to not have column headers and then everything will come in as F1, F2, F3, etc... You can then easily union based on column position. You'll just have to rename the fields once the union is complete and filter out the headers that did come through on the sheet/file that had them.
6. You should be able to split the field based on a line break -- try calculated fields like
SPLIT([field], char(10)), 1)
SPLIT([field], char(10)), 2)
Then you can pivot those into rows.
7. Do you mean a Change within a Step to another Step? I agree this would be a very useful feature. Please vote for it here: https://community.tableau.com/ideas/9133
8. I've not tried, but try SHIFT + Enter. I don't know if it's supported.
9. Not currently possible that I know
10. This would be a very useful feature. Please vote for it here: https://community.tableau.com/ideas/9394
11. This is actually a very good question and deserves more thought and consideration than I can add here. I'd love to see some features included in Tableau Prep that give a better picture of lineage and even some smart automatic checking of data (the suggested data roles and fixes are a move in that direction - but a much more robust checking throughout would be awesome!) Right now, I find myself checking my output against my input and accounting for logic - but that's not always easy, precise, fast, or in some cases even possible.
These are some quick answers to your questions. If any of your questions didn't get the complete answer you were hoping for, please start a new thread for that specific question so we can all go deeper into finding solutions!