As much as it's tragic for the Ummah to be divided into 2 sects, the Quran says there should NOT be any sects in Islam. Shias and the Sunnis should call themselves Muslims, the only name recognized in the Quran.
To start with, we should all remind ourselves of this Quranic verse and ponder over it:
"As for those who divide their religion and break up into sects, thou hast no part in them in the least: their affair is with Allah. He will in the end tell them the truth of all that they did." Holy Quran 6:159
There are a number of differences in the Shia and the Sunni Juristic opinions. But these differences cannot be termed as the "basic differences" in these two (unfortunately) major sects of Islam. The basic difference in the two sects is that of the Shiite faith of the system of "Imamat". The Shiite faith of "Imamat" implies that after the Prophet (pbuh), there shall be no other prophet, but the only true leader of the Muslims, at a given time, is an "Imam" who, like the prophets of Allah, is directly appointed by Allah. The appointment of the first "Imam" was made by Allah through the last prophet (pbuh) and every subsequent "Imam" is appointed by Allah through the "Imam" who precedes him. Another qualification of the "Imam", according to the Shiite belief is that he shall belong to the family of the last prophet (pbuh). In this category, the khilafat of first, second and third caliphs of Islam are held null and void and done out of wrong-doing to the Ummah. The Shiite belief holds that the "Imams", like the prophets of Allah, are "masoom" (sinless, innocent) and therefore should be obeyed in all matters and under all circumstances. The "Imams", according to the Shiite faith, are thus not just the political leaders of the Muslims but also their religious leaders and clergy.
The Sunni school, on the other hand, do not hold any such belief. Sunnis believe that when the Prophet Mohammed (SAW) was dying, he ordered Abu Bakr (the first Khalifah) to lead the prayer. Muslims understood the order of the Prophet that Abu Bakr should be the first Khalifah.
Are these differences between Shias & Sunnis basic difference in Islam? Are these differences basic and threatening to faith (Iman) or just trifle? Why do some scholars from both sides call the other as non-Muslims?
Yes, I do NOT agree that the difference in the Shiite and the Sunni sects are quite basic, and I think there is still no need to fire each other′s emotions to such great extents, even if someone thinks differences are so grave. We Muslims must be united. We must be one hand, one body, one heart, one mind and one word. We have the same God, the same last Prophet (SAW), the same Mecca, the same prayers, the same Ramadan, the same goals, the same destiny and the same enemy. True Muslims do not allow anything to create disunity among them, because Allah (SWT) Has repeatedly prohibited divisions among believers
"Obey Allah and his Messenger, and fall into no disputes, losing your heart and your power, and be patient, surely Allah is with those who are patient" Holy Quran 6:159
"Be united by holding onto God's Covenant, and do not be divided" Holy Quran 8:46
"The believers, men and women, are Auliya (friends) of one another" Holy Quran 9:71
"Do not be like those who are divided among themselves and fall into disputations after receiving clear evidence; for those (who are divided) will be a great punishment" Holy Quran 30:31, 32
"The believers are brothers, make peace between your brothers, and beware of Allah, that you may receive mercy" Holy Quran 49:10
"O Lord, forgive us, and our brothers who came before us into the faith, and leave no, in our hearts, any animosity against the believers" 59:10
The Prophet Mohammed (SAW) said: "A Muslim is the brother of every other Muslim; he doesn't do him wrong and does not abandon him. Whomsoever comes to the aid of his brother at the time of need, Allah will aid him at his time of need. Whomsoever lifts a burden off of his brother, Allah will remove from upon him a burden from burdens of the day of judgment".