Why are these features missing in modern day general purpose computer languages?
You are asking a lot of questions, here are quick answers on some of them:


Syntactic sugar for integer literals: in a language like C, commas already have a function (they are an operator on their own), so there would be an ambiguity. Other languages allow them. In many countries in Europe, the roles of , and . are switched, and this highlights the fact that this type of issue is best handled by a preprocessor.
Large integers: operations on larger integers are slower than ones on smaller integers, so it makes sense to have different types in many circumstances. Libraries typically provide support for large integers even if the language doesn't natively support them.
Math library lacking support for your favorite functions: everybody's favorite functions are different. There is probably a library that supports yours, and otherwise you can write one. Computer algebra systems tend to support all mathematical functions you will ever want to use.
Indentation: you might like indentation, others might not. Generally speaking, the rule in most programming languages (other than Python and perhaps a few others) is that whitespace shouldn't matter. There are many reasons for that, including (historically) macro expansions (or INCLUDEs), and differing indentation styles. If you want to enforce your type of conventions, use a preprocessor.
Built-in profiling: many C compilers already have this feature, and it is part of the tool chain in most widely used programming languages. There is no need for explicit support in language syntax.


In general, one can think of many "improvements" and features for programming languages. That is one of the reasons why there are so many of them. Different compilers might actually implement some of these, perhaps optionally. To answer your general question, why your favorite feature isn't part of your favorite language, the answer is twofold. First, there are many potential features, and programming languages cannot implement all of them (see for example the recent C++ standards, adding lots of features and making the language ever harder to learn). Second, there are some performance issues that you might be ignoring.