now, when you create your huge application based on kixtart that uses those scriptlets, you currently need to remove all the include lines from all the files and add them to the main file
No you don't - I've been using conditional CALLs as a replacement for #IFDEF / #INCLUDE in main and sub-scripts ever since we got IsDeclared().
It is only a problem if you are going to tokenise the main file and the included scriptlets, otherwise the combination of CALL and IsDeclared() will do the job just as well.
In fact CALL is the generally going to be the better option, as you can use variables and macros in the path which can only be determined at run time.
The only other reason that I can think that you need include is if you want to declare local variables that you are then going to use in the main script. Not a good idea IMO.