The abovementioned question is actually comprised of a number of questions:

Is it true that the hadith in which the Imam says that Abu Bakr and Umar are best individuals among the Ummah after the prophet, is mutawatir (narrated so many times and by different transmitters, to the extent that one becomes sure such a hadith has indeed been issued by an infallible)?

How come the Imam did not oppose and object to the previous Caliphs and did not declare them kafirs and announce that they had unrightfully usurped the Caliphate when he came to power?

Why didn't he take act on his own opinion regarding issues like temporary marriage, the garden of Fadak, tamattu’ hajj and the adhan and why didn't he bring a new Quran for the Muslims?

If Imam Ali did not do any of  the abovementioned acts, should we believe that he betrayed the Ummah?

Before explaining the answers to these questions we must note that such questions come to mind, due to the fact that the Bani Umayyah (the Umayyids) prohibited the narration of any hadith mentioning the virtues of Imam Ali and altered history because of political ambitions, which unfortunately is still going on due to the same reasons. But before explaining the answers we advise you that if you are really seeking the truth and you are not aiming to cause conflict between Sunnis and Shias--which is to the best interest of the enemies of Islam--then you can, without prejudice, refer to the theological books that have been written by Shia Scholars and understand the truth. You should be sure that "Those who strive in us, we shall surely guide them in our ways"[1]

Regarding the hadith you cited from Imam Ali we must say that even if such a hadith is mutawatir  in Sunni hadith records, it is definitely not so in Shias hadith books. In fact you cannot find one Shia hadith book that has narrated this hadith and as you know in scholarly arguments, you can only support your opinion with a hadith that both sides of the debate consider mutawatir.

For example, the following issues can be considered mutawatir for both sides, as they are mentioned in both Sunni and Shia sources. Here, we will only refer to the books of our Sunni brothers because that is all that is needed for our aim:

1- The hadith which says that Imam Ali's relation towards the prophet is identical to that of Prophet Harun's to Prophet Musa.[2]

2- The hadith in which the prophet said: "The person that angers Fatimah is like the person who has angered me."[3]

3- The fact that an individual did not let the prophet write something at the end of his life and claimed the prophet was hallucinating.[4]

4- The fact that Fatimah (as) was dissatisfied with the first and second Caliphs until she passed away.[5]

5- The fact that the prophet replaced Abu Bakr with Ali to convey the message of Bara'at.[6]

6- The fact that the first and second Caliphs raised their voice to the point that they were scolded and chided by the first verses of Surah Al-Hujarat[7], although the Sunnis believe that they were forgiven later on by Allah.

The abovementioned issues and tens of others among them can be identified as mutawatir ahadith for both sides, because not only have they been mentioned in Shia books but they are also mentioned in the most authentic and verifiable books of the Sunnis such as Sahih Bukhari, which is considered the sister of the Quran from their point of view, and by scrutinizing these ahadith one can conclude that they clearly contradict the hadith mentioned in the question. Regarding the hadith that you claimed to be mutawatir, it can be said that after the reign of the previous Caliphs, the heads of the Umayyids which were foes of Imam Ali (as), tried to promote the idea of Abu Bakr and Umar being the best people after the prophet, putting Ali after them.  Continuing the same line of propaganda, they eventually imputed this hadith to Imam Ali so that it would seem more reliable.

In this regard there is a hadith narrated in Shia books that even if one does not accept the chain of narrators he must accept the argument mentioned in it:

Abu Khalid Kabuli says: "I told Imam Sajjad: People[8] say that the greatest individual after the prophet is Abu Bakr, then Umar, then Uthman, and then Ali. The Imam replied: If this is true, then how do they explain the hadith Saeed Bin Musayyeb has narrated from Sa’d Bin Abi Waghas in which the prophet has told Imam Ali: "Your relation towards me is identical to that of Harun's to Prophet Musa, except that there is no prophet after me."[9] Was there anyone closer to Musa than Harun at that point?"[10]

Through this hadith (the hadith of Manzilah) which is considered authentic by both Shias and Sunnis, the imam indirectly assured that the hadith that had spread among the people and was attributed to Imam Ali was nothing but a forged one. This argument seems reasonable regardless of who has said it.

As for why the imam did not oppose and object to the previous Caliphs one must say that from the Shia point of view and according to what has been cited in our books, the imam has expressed his criticism and opposition towards the previous Caliphs. The sermon of Shighshigiyyah is  a good example of such criticism.

Based on what is mutawatir for both Sunnis and Shias, we pose some questions:

1- Isn't ousting Mu'awiyah (who was assigned by the previous Caliphs) from the government of Sham a means of opposing their decision?

2- Isn't distributing the wealth in the public treasury in a new manner considered an act of opposition?

3- Isn't focusing on improving the Islamic society's spiritual situation instead of continuing to conquer foreign lands a change in policy? … and other examples of this sort.

It is known that even during the reign of the previous Caliphs he was perceived as an individual that criticized and opposed the government. We pose one of the many examples as a question to you: why did he not give allegiance to Abu Bakr, which you claim to be the greatest person after the prophet, until his wife Fatimah passed away and was buried at night?[11]

Of course on some occasions the Imam would assist the Caliphs in resolving problematic issues in the Islamic society[12] despite the many objections he had, in order safeguard the essence of Islam. Or as he states wonderfully: "We have a right. If it is allowed to us well then so be it, otherwise, we will ride on the hind of the camel as the number two person, even though the night journey may be long."[13]

The truth of the matter is that the imam viewed power and authority as a means rather than an ends, and for this reason during the reign of the Caliphs and even during his apparent Caliphate he preferred to remain silent about many issues and let the next generations judge for themselves.

Pertaining to the kufr (disbelief) of the individuals you mentioned we must note that from the Shia point of view anyone who says the Shahadatein is considered a Muslim, (therefore Shias believe that the previous Caliphs were all Muslims).

Regarding why the imam did not act on his own opinion about many issues, it's interesting to know that during the time he had authority, as you put it, he did oppose the Tarawih salat that was commonly practiced, but because of the objection of a group of people he was forced to leave them to themselves[14] and you must surely know that he did not agree on Abu Musa Al Ash'ari being chosen as one of the arbitrators but once again he was forced to agree It is easy to forget that when he became the Caliph it had been 25 years since the Muslim society was constantly brainwashed and influenced by the propaganda that justified the actions of the previous Caliphs and to oppose them in some fields would cause serious problems. For example, returning Fadak was perceived as an effort to reach personal interests.  Moreover, the period of his Caliphate was so short and full of battles and sabotages that would not give him the opportunity for fundamental reformation regarding many issues.

Regarding the Quran and why he didn’t bring a new one, one must say that Shias accept the current Quran and believe that it has been revealed by Allah, but they also believe that the Quran Ali was presenting not only consisted of the current Quranic text, but as a supplementary (and not part of the Quranic text), it included many other things, such as the knowledge of the Nasekh and Mansookh verses the occasions of revelation and many interpretations and explanations. However, because of the reasons we mentioned before he was not able to present this work to society, in which there were naive people that were deceived by the enemy's army when they put Qurans on the top of their spears. As a result they rejected to obey the Imam and did not pay attention to his statement: "I am the closest person to the Quran."[15]

In regard to the last part of the question we must explain that remaining silent is not always betrayal, in fact the only silence that is betrayal is one that if broken will cause the society to thrive and progress, not to exacerbate the society's corruption.

As a few examples we will pose some questions:

1- Did the prophet betray the Muslim society when he decided to perform prayer for the body of the famous hypocrite Abdullah Bin Ubayy without heeding to the second Caliph's opinion?[16]

2- Was the silence of Prophet Khidr about the logic behind his actions at the beginning of his journey mentioned in Surah Al Kahf, a means of betrayal to Musa?

3- Does the fact that Allah could have introduced the hypocrites to the prophet according to verse 101 of Surah Al Tawbah and verse 30 of Surah Muhammad and that the prophet did not ask Him to do so, indicate that both Allah and the prophet betrayed Islam and the Muslims?

4- Was the silence of Prophet Harun regarding the worshipping of the Calf by Bani Israel (The Israelites) and excusing this silence by arguing to Prophet Musa that they thought he was a weak man and threatened his life a way of betrayal?[17]

None of these were seen as betrayal and similarly, the silence of Imam Ali (who has the same status as prophet Harun in relation to Musa) regarding some issues cannot be considered betrayal due to the situation he was dealing with where three different groups of Muslims were in conflict with him and other groups were opposing his policies and finally martyred him. Instead it is the responsibility of you and us to find the truth through objective research.