What's wrong with R5RS?
It doesn't define a standard module system or macros (beyond syntax-rules), exceptions, or record types. Most R5RS implementations offer those, but they're all different and incompatible. The standard also doesn't help with boring but necessary stuff like file encodings, character sets, etc.
So instead of writing a (nontrivial) program for R5RS Scheme, you have to write it for MIT Scheme or Racket or Chicken or Chibi or ...
I'm all for recommendations on things like those, so if you chose to implement them, there's a standard way, but I'm not in favor of making those part of the standard.
Not really. Exceptions are easy to build on top of continuations, which are already part of R5RS.