Did the Buddha speak the Mahanidana Sutta in the Digha Nikaya? In the Pali suttas, there are scores of suttas about Dependent Origination which take the classic form of the 12 links, the benchmark being SN 12.2. 

In the Digha Nikaya, there is the Maha-Nidana Sutta, called the 'Great Cause'. I find the name of the sutta strange since if it is 'great', why are there only 9 links instead of 12?

While there are many suttas containing less than 12 links, it seems strange the Maha-Nidana Sutta omits the six sense spheres, which the Buddha described as one of his core teachings in AN 3.61 &amp; are central to so many suttas on Dependent Origination (such as MN 18, MN 38, MN 148, etc). 

More importantly, the Maha-Nidana Sutta defines consciousness &amp; nama-rupa differently to other suttas. In the Maha-Nidana Sutta, consciousness (which is only mental cognition in other suttas) is said to descend into the womb of a mother. Nama-rupa has a Brahmanistic meaning of 'naming-forms'. 

Also, 'birth' refers to the birth of different animals &amp; creatures rather than the birth of "beings" or "satta". SN 23.2 refers to a "being" as a mind that is attached to the five aggregates as "self". It is doubtful birds &amp; snakes conceive the five aggregates as "self" or generate "self-views" of "beings" (as described in SN 5.10). 

Are there any compelling reasons or grounds why Buddhists should accept the Maha-Nidana Sutta of the Digha Nikaya as the words of the Buddha?
It is true that Maha Nidana Sutta in the Digha Nikaya points out Paticcasamuppada  (the process of Dependant Arising), and of Nāma-kāya Rupa-kāya - (mentality and materiality) together with vinnana (consciousness) somewhat different to some other suttas.  Paticcasamuppada is the most important of all other related teachings. It is a deep and complex doctrine, and understanding this is Key to seeing the Truth. So one cannot rule out Maha Nidana Sutta in the Digha Nikaya by just such observations as that you’ve pointed out. We should remember well Buddha’s words:


  By not understanding, and not penetrating this doctrine of Paticcasamuppada, beings have become entangled like in a knotted ball of thread and have become like munja grass and rushes, unable to pass beyond the woeful states of existence, and Samsara, the cycle of existence.


For Buddha to exclude Ignorance, Volitional Activities, and Six sense-bases, there is a reason. It is just that you and I have not yet found out as to why it is so.  In Maha Nidana Sutta it is said: 


  "Thus, Ananda, from Nāma-Rupa as a requisite condition comes consciousness. From consciousness as a requisite condition comes Nāma-Rupa. Then from Nāma-Rupa as a requisite condition comes contact..."


It was shown thus because one cannot exist without the other. The Buddha showed this with an example of two bundles of reeds to make it easy to understand. Two bundles of reeds are kept on the ground with a little space between them leaning against each other with their top ends, that both the bundles are kept standing with the support of each other. Removing one removes the other. 

I will try and find the answer to your question within the month, but let us keep in mind that learning is a gradual process. The Buddha said that his method is gradual training, gradual action and gradual practice. So I will look into ‘Pancha Bhaya Wera Sutta’, ‘Nalakalapa Sutta‘, ‘Loka Sutta’, ‘Maha Nidhana Sutta‘ etc. on Paticca Samuppadaya. 

Until we find a proper answers let us not discard any of the original suttas. Let us not put away what we feel are contradictory statements till we have understood thoroughly the fundamentals. Only if when we detect the structural principles of such paticcasamuppada links, in the entirety of the teaching, then you would have arrived at the true Dhamma. So let us try to dig a little deeper.