Option for a 100 percent manual notation editor (like Finale)

To start by stating the obvious: MuseScore is not Finale ;-)
This is not meant as a rebuke of any kind. It's just that different notation software uses different approaches to their workflows. If you try to use MuseScore the Finale or the Sibelius or the Encore or the [insert program here] way, you'll always be surprised by some seemingly similar functions/tools that work differently. That being said, it can't hurt to look at what makes those programs and workflows "work" for their users and see if some of those methods may/should be incorporated.

You've touched on quite some points, I'll try to address them all from my viewpoint as a fairly advanced user that also has some familiarity with parts of the code.

1. The flat or sharp option clicking off after I place one note - If I didn't want to keep using the flat or sharp tool, I would have turned it off myself.

To me, not having it turn off after entering a pitch would mean hundreds if not thousands of additional clicks/keystrokes when entering scores. The times I need to enter successive runs of flats/sharps is way less than the times where it isn't.
I guess this probably relates to the type of music one is writing, so perhaps a way to make this a "sticky" setting during note entry could make sense. It would be interesting to see how many other users would like this.

2. The dot tool disables every time I change which note I am using. So, I click the dot option, and click a quarter note. Then I decided I want a dotted eighth note instead. When I change my note from one kind to another, the dot gets unpressed. Then I have to re-select the dot option. Why is this necessary?

Because the dot "tool" isn't a tool at all. It is an integral part of the note duration. So when you change note duration, that is exactly what happens, MuseScore changes to duration to what you're asking it.
Note that there are specific halve/double duration commands (default shortcuts Q/W) that will retain the dot information, but they work post-entry (even in note entry mode)

3. The tie tool is a disaster. It won't light up when I click on it. Instead of letting me place a note with a tie, it just puts a tie on the last note I placed, along with placing another note identical to the note that my mouse is holding. The note on my mouse doesn't even preview with a tie. When I go back and click on the note I wanted to tie, it STILL puts the tie on the last note I entered. Is this tool broken?

It is most definitely not broken.
During Note entry mode, the tie command will insert a tied note with the chosen duration alongside with the tie, starting from the currently selected note/chord. Which even works for chords all at once.
Outside of note input mode, it will behave as you tried to use it. Adding/removing a tie to the selected note/chord.

4. There seems to be a glitch where the rest tool gets stuck as being on and I can't go back to notation mode. I have to click off the page to reset everything and then click a note to begin inputting again. That is weird.

That would be weird indeed; so far I've been unable to reproduce such behavior. I can always just unclick the rest button in what I've tried so far.
Though, even for mouse entry you don't even have to turn on the rest input toggle, as simply right-clicking inserts a rest as well.

5. Buttons for each type of rest and for triplets would be nice.

Some people have indeed asked for the duration buttons to switch to rests if/when the rest button is enabled. I personally don't see the added value from this at all. I'm not against it either.
I do wonder though why all those people never request that those duration buttons also change to (single/double/triple/quadruple) dotted variants if they press one of the dot buttons...

For tuplets, a toolbar button is included in the UI design proposal for MuseScore 4.

6. A tool like Finale's measure tool would be great. It lets me highlight entire measures with one click, copy and paste them with just a mouse, and delete them to either get rid of the notes or reset the rests so it looks like a clean empty measure.

Click an empty space within a measure and the full measure becomes selected: didn't even need a tool for that ;)
How do you then copy-paste that measure with the mouse?
Once the measure is selected, the delete command indeed gets rid of all the contents and shows the measure rest instead; not quite sure what your missing here?

7. Overall, I don't really like the keyboard shortcuts necessary to use certain notation features.

I don't think there are any keyboard shortcuts required at all and everything (aside from typing text) can be done with the mouse; so please elaborate on which notation feature you currently miss from the mouse.
Personally I love not having to use the mouse very often, as I've found keyboard entry to be much faster (admittedly, it has a learning curve). I very much oppose functions that are only accessible via the mouse as it would likely exclude blind users to discover and use them..

8. and the blue highlighter thing is not very useful when writing for large ensembles and going back and forth between staves.

I'm not sure I get which blue highlighter thing you're referring to and how it impedes writing for large ensembles and/or going back and forth between staves.

Depending on how you write for your large ensemble it could be worth temporarily hiding some instruments (I usually work by section) to make navigation a bit easier.

Hopefully this post explains some of the reasoning behind the behavior you've experienced as different/less expected.