It is not clear what you mean by problem 1. The equation numbers are inserted by Maple automatically, as undoubtedly you noticed. You do not get to pick these. If you put an equation into your section, they will be (1.1), (1.2) and so on.
If you refer to a forward reference; i.e. referencing 7 before you get there: Maple does not know these numbers until it evaluates the line. So you cannot reference (7) before Maple has actually assigned it.
Problem 2 is easier: The boldened words are Maple keywords. The italic print indicates that you maybe in an evaluation group. Maple would try to evaluate the section (hit the !!! button to see what it is doing). Since you work in 2-D input mode you can use F5 to switch between text (no evaluation, typeset in roman) and math (evaluation, typeset in italic).
Be aware that Maple also has 1-D input mode; much easier to use if all you want is to perform a calculation. In the Prefs, Interface tab, set Default format for new worksheets to "Worksheet" and on the Display tab, set Input display to Maple Notation. Of course if you want the typesetting you want the Document type and 2-D input.
I don't know Mma well, but I do not see where Maple lacks flexibiility with the exception of list and array handling, where Maple is much more strongly typed: it has lists, Vectors, Sets, Arrays, Matrix, ... whereas for Mma apparently most of these are lists.