How does one improve the typesetting of a document? There are no straightforward answers. Traditionally a number of craftsmen and professionals were involved in the publishing of a book. With what is now called "self-publishing" all these decisions now fall on the author's shoulder. The disappointing results can be viewed at Lulu.com
Do you have to read the manuals? Unfortunately yes, if you want to manipulate and be in control of what they do. Unfortunately there is no package available called "bettertypography" and the reason is that typography and typesetting have no fixed rules. Whatever rules could be deduced (about 100 are already programmed into (La)TeX) the balance are for you to define. Asking that a piece of software can produce art or a book design is not possible or feasible.
Typesetters have their origins as craftsmen working alongside the printer but the rise of desktop publishing has democratized this work and thus eroded the typesetter’s status.
A typesetter needs to have flair and an artistic eye (hence why the jobs of typesetter and book designer are often combined). But the work also demands meticulous attention to detail and application of uniform standards.
When you decided to produce your publication you have accepted the role of the typesetter. You need to invest adequate time to learn about typesetting and computer programming.
There are no-shortcuts and instant solutions. No magic wands. You need to invest time in effortful study.
Having said all that, a good class can go a long way to save you time. For example most Journals offer their own classes and the majority of authors do not have to worry much about the final look of papers (although the editors, might add some modifications). The most important decision you make, if you are unwilling to invest time in disciplines that are not within your core of expertise is to choose your class carefully.
Will future LaTeX distributions be more complete and user-friendly?
Software in general evolve by adding more abstractions and more complexity. LaTeX3 is expected at some stage to provide a more "complete" typesetting and programming framework. More user-friendly? Highly unlikely.
What date should I use for fixltx2e, and where do I find it?
Find the file fixltx2e.sty on your computer open it up in your text editor and the date is stated by the Providespackage command:
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{fixltx2e}
[2006/09/13 v1.1m fixes to LaTeX]
If you are not going to distribute your raw file to anyone, don't worry about the date, just don't use any date, everything will still work fine.
Microtype
The final option is the default (like in most classes), unless you use draft in your class. In that case you will have to explicitly state it. From the manual:
E.g., if you are using the class option draft to show any overfull
boxes, you should load microtype with the final option.
User friendly compiler errors?
Software developers think that error messages they build in their software are user friendly.
In most cases they are as user friendly as calculus.
Have I missed something in the manuals?
This is not a hard one to answer. If you did not read the manuals you probably did.
Do you know more? are all of these things always a good idea?
Probably and yes they are a good idea.
BONUS
How to Ask a Question
The questions with more left unsaid than said normally go ignored. A question that is not very focused will not elicit many answers. State clearly what you expect to gain from the answers.
Ask one question at a time.
Get people interested in answering your question. It is almost like you are making a sale here! "Hey, look at my question, I’m obviously interested in helping you give me an answer so pay attention to me". Provide a minimal example and ask how to better it or why it does not work. When your question starts with one of Kipling's six honest men you will receive better answers.