Manipulation of shapes.
Kidding, but let me explain it to you.
1. At what point do we say a jutsu comprises of shape manipulation?
When you visually see the chakra manifested in the image of how the user wants it or intends to use it.
Perfect Examples: Rasengan, raikiri, BM mode, Tailed beast bombs etc, Susanoo:
All these abilities use pure chakra which by itself is nothing. However once it's shaped and defined how the user wishes they all become quite deadly.
If Sasuke and Madara used a massive cloud of chakra with no form or density it wouldn't do much. However, once they mold it into Perfect Susanoo it's extremely powerful.
2. Why is it so hard to combine it with nature manipulation?
Multitasking / Body limitations:
A) When you do shape manipulation. You are manifesting chakra from your body and shaping it to what you want.
B) When you do Nature manipulation. You are taking chakra from your body and converting it to your specific nature.
C) Maintaining both A and B.
When you try to combine both you are essentially:
Maintaining A
Creating B while maintaining A
Then concentrating on Combining A and B perfectly while maintaining them both.
Essentially if the chakra required to perform the task doesn't limit you. The concentration or maintaining the jutsu will limit you.
With the current state of the series I believe some of the higher end characters can perform this now as:
1) More chakra
2) Better chakra control
3) Nature affinities are maxed or amazing at this point.
Obviously Naruto and Sasuke can do this but im referring to characters like Sakura, kakashi, etc. Im positive Sakura could do it if she had an affinity
3. What would you consider exceptions to your own stated rules on this?
JJs, Riku characters and anyone with:
KKGs/KKTs/KKMs
Massive amounts of chakra to sustain jutsu (Kurama Jin)
Perfected Nature affinities (Rinnegan users)
Secret jutsu with secret practices (Dust release)
For Fun: Cookie dough explanation
1. At what point do we say a jutsu comprises of shape manipulation?
The point at which you visually see the raw cookie dough forming or being shaped to what you want.
2. Why is it so hard to combine it with nature manipulation?
1) You shape a perfect normal cookie with cookie dough using both hands.
2) You now want to shape a chocolate chip cookie in your right hand while maintaining the first cookie in your left hand.
3) You use 1 hand to shape the chocolate chip cookie while maintaining the other cookie in your left hand.
4) Now with both cookies molded you want to combine them together without either one breaking apart.
The whole issue I have with this is that IMO techniques like explosive bubbles, earth dome, fire/water dragon, water shark, all wood tech, etc. would all logically require both nature and shape manipulation simultaneously. What then makes that feat such a significant feat when Naruto pulled it off, seeing as even some genin have shown prowess with some of these techniques.
Because you technically aren't combining two jutsu simultaneously. it's one affinity and for those that do have two affinities or more they are KKGs/KKT/KKMs which are blood line limits that "Creates" the qualifications required to perform the jutsu without much effort from the user.