Even mainstream Shias believe that Mola Ali (a.s.) was present on Arsh when Prophet (s.a.w.) went for Meraj :-
Ibn babawaiyah qummi narrates from jafar: prophet(saw) went into the skies 120 times , everytime allah made the wahi of wilayat of ali towards prophet(saw), so many times the wahi regarding wilayat of ali was done that no other farz was given such priority.( muqadma tafseer al burhan , pg 22).
When prophet(saw) went into the skies in the night of meraj , he saw ali had already reached there before him, he greeted him , while he had left him on earth.(tafseer al burhan vol 2, pg 404 from barsi)
In One more rivayat from saduq, in al amali.
When (on the night of meraj) I was taken in to the skies, I got closer to my lord, such that there was just a gap of two pillars or less than that, between us. Allah said: oy muhammed, whom you love the most among the creatures, I replied ali. Allah said, see over there muhammed!
I saw on my left side there was ali(a.s) present.(tafseer al burhan vol 2, pg 404 from barsi)
In the book Kashf al‑Ghummah, it has been narrated from Abdullah ibn Umar that: "I heard someone ask the Prophet of Allah , `With what voice did Allah, the Glorified and High, speak to you in on the night of the Me'raj?"
The Prophet replied, "My Lord spoke to me with the voice of 'Ali ibn Abi Talib and said, `O' Ahmad! I am an Entity that is not like anything else. I can not be compared to anything else and I know all the secrets of your heart. With the exception of 'Ali ibn Abi Talib , you have no other close friend. Thus, I speak to you with the voice of 'Ali ibn Abi Talib so that your heart will be at ease.""
From Kashf al-Ghummah, Vol. 1, p. 106, Fee mahabbati al-rasooli (s) iyyahu wa tahreedahu alaa mahabbatihi wa muwaalaatihi wa nahyuhu an baghdihi.
Also in the Hadith Book Bihar al Anwar vol.9 page 76 it is narrated from Imam Sadiq a.s. that prophet said:
when reached where there was nothing between me and Allah and there was no angel or prophet. I did not asked anything unless I received better of it. at that time this came to my mind:
You are only a warner, and for every Ummah is a guide.
http://tanzil.net/#13:7
so I asked Allah: O my trainer you placed me Warner. but who is Guide of my Ummah? Allah replied O Muhammad! he is Ali Ibn Abi Talib. he is guide and leader of who found my way and who are pious...
Also these hadiths are narrated in Bihar al Anwar
“It is related that Muhammad declared that on the night of Ascension, the Most High commanded me to inquire of the past prophets for what reason they were exalted to that rank, and they all testified, “We were raised up on account of your Prophetical Office, and the Imamate of Ali Ibn Abu Talib, and the Imams of your posterity”. A divine voice then commanded, ‘look on the right side of the empyrean’. I looked and saw the similitude of Ali, and Hasan, and Husain, and Ali ibn al-Husain, and Muhammad Bakir, and Jafar as-Sadiq, and Musa Kazim, and Ali ibn Musa-ar-Reza, and Muhammad Taki, and Ali Naqi, and Hasan Askhari, and Mahdi all performing prayers in a sea of light. ‘These’, said the Most High, “are my proofs, Vicegerents, and friends, and the last of them will take vengeance on my enemies.”
and
‘The Prophet declared that when he performed the Ascension, the angels inquired very particularly about Ali. ‘When I arrived,’ he continued, ‘at the fourth heaven, I saw the angel of death, who said that it was his office to take the soul of every creature by God’s command; but in the case of you and Ali, I will have to take your consent.’ When I came under the empyrean, I saw Ali ibn Abu Talib standing there, and said to him, ‘O Ali have you got there before me?’ ‘Whom are you addressing’, asked Gabriel. ‘My brother’, I replied. ‘This is not Ali,’ said he, ‘but an angel of the Merciful God, whom he created in the likeness of Ali and when those of us privileged to approach near the Deity wish to behold Ali, we visit this angel.”
and
And so Jesus and Moses and Abraham all inquired about Ali and congratulated Muhammad on having left so good a Caliph in his place. The Apostle further related,
“On the night of MERAJ, on every one of the curtains of light and on every one of the pillars of the empyrean to which I came, I saw written; there is no God but Allah, Muhammad is the Apostle of God, and Ali ibn Abu Talib is the commander of the Faithful.”