While most of what you say is pretty true, you also clearly are not aware of one extremely handy shortcut.
When you hover over a commander and press Ctrl+M it takes you to the casting menue, but you are there to choose a 'Monthly ritual'. this is a ritual your guy casts every month, so long as you have enough gems for him to begin casting the next ritual as soon as you finish this one. so a 1 cost ritual you need 2 gems one to cast this turn's and one to begin casting next turns.
This is useful for monthly summoning troops and for monthly casting site searchers. for the latter the AI chooses a new site every month, and is pretty good at it. it searches them in numerical order but skips capitals and skips partially searched sites until it is out of unsearched sites.
to know what a summoned unit is going to be or what a mercenary looks like you need the wiki:
http://dom3.servegame.com/wiki/Main_Page
basically press the windows button, look it up on line, then change back to domIII. a bit annoying but better than summoning in the dark,
since I already have a long schpeal, I may as well answer your questions:
1. some magical items boost your skills in a magic path.
http://dom3.servegame.com/wiki/User:..._booster_guide
2. Its an absolute nightmare. Nature, Water and Air magic all have magic items that you can forge that allow you take different numbers of troops into the drink. you can also recruit water breathing indies. a lot of late game summons are amphibious. or dominion kill the under water guy.
3. Most commanders aren't effective in malee, and theres nothing you can do about it. the only way to make them useful at all is give them a magic item that gives them something to do, like a bow.
for those who are actually good fighters, you have a number of options: have them attack alone, put them in the front line, put them on a flank where no one will get in their way, or give them flying. I'm sure there are other strategies I'm not thinking of
4. This is a huge issue, that I'm not going to cover. loads of stuff on the wiki, on the forums and in the manual.
5. Every fort exerts a tax of resources from neighboring provinces, a percentage of their overall resources. It can't do this to another fort, though. so if you put a fort next to your capital, that one less provence that the capital is taxing the resources of. If you surround your capital with forts, it will only have the resources it can get from its own square, which is a small fraction of the resources it would have otherwise.
6. Healing is really hard but doable, you need to find a commander with the healing ability, of whom the easiest to get is her:
http://dom3.servegame.com/wiki/Faerie_Court . Its impossible to dismiss troops.
7. Yes (with a few exceptions)
should have expected to get ninja'd, i took so long writing that