The nature of Lord of Tirumalai has always been a matter of discussion.
Disputes about Nature of Lord Venkatesvara
"Is Lord Venkatesvara of Tirumalai a manifestation of Vishnu of Siva? Is He manifestation of Subramanya Swamy or Shakti? These are the questions which time and again agitate the minds of the devotees. ... Shri Vaishnavas hold that the Lord is Vishnu and Vishnu alone, while Shaivas, who see in Him their Ishta Daivam Shiva, hold with equal enthusiasm that He is Shiva. Some again hold the view that the image is that of Skanda. A few Sakti worshipers also believe that the deity is Parasakkti. Several devotees of the Lord are again of the view that He is the combination of Vishnu and Shiva elements and is in fact a Hari-Hara murthi. There are again others who hold that Lord Venkatesvara is manifestation of Paravasudeva." [Sitapati: 21]
Court Disputes in 11th or 12th century A.D.
Sitapati gives an account of the court proceedings that took place in 11th or 12th century A.D., the details of which are important. He observes:
"The controversy about the Hara nature of the Lord was actually argued by the contending parties in the 11th or 12th centuries A.D. before a Yadava Raja of Narayanvanam in the Jaykonda Chola Manadalam. The Sri Venkatachal Itihas Mala, a Sanskrit work of the 12 th century, describes in detail in the first three stabakas a scholarly discussion carried on at a high intellectual level long long ago, between the Vaishnavites led by Sri Ramanuja and the Saivites about the nature of the Lord's image at Tirumalai - whether it was a Shaivite image or the image of Vishnu..." [Sitapati: 21]
Points against it being Vishnu as argued by Shaivas
"The image of the Lord in Tirumalai is that of Skanda or Kumara Swami. The holy Pushkarni on Tirumalai itself is therefore called Swami Pushkarni. Swami is really an appellation commonly used for Skanda or Kumara Swami. The shortened form 'Swami' is used instead of calling the Pushkarni 'Kumara Swami Pushkarni'. It is not unusual for nouns to be used thus in the shortened from. For example, the nouns Bheema sena and Satya Bhama are usually used in the shortened forms as Bheema and Bhama. The Vamana Purana also mentions that Skanda performed penance on Venkatachala on the advice of father Siva. The image of the Lord at Tirumalai is that of Skanda and not Vishnu, Venkatachalam is primarily a Varaha kshetram and as Vishnu has already manifested Himself here in the Boar from, the image of the Lord at Tirumalai can only be that of Skanda.
"The image of the Lord has not got the characteristic weapons of Vishnu such as the Chakra and the Skanda came to perform tapas on the banks of Pushkarni and has manifested himself without his weapons or his extra hands. Vaishnavites had taken possession of the temple of Subramanaya and had converted it into a Vishnu temple. The presence of the matted locks or jata jutas on the image and the Nagabhushanams (snake ornaments) prove that it is a Saivite image. Puja is also done in the temple with 'bilva' leaves; bilva are used only for worship in Saivite temple and not used for Vishnu worship. The image has also a crescent mark on the head indicating that the image is Siva if not Kumara Swami.
Points in favour of it being Vishnu as argued by Vaishnavas
"The term 'Swami' need not apply to Kumaraswami. It only means that Swami Pushkarni is the 'Swami' in 'tirthams' and thus a Lord among the holy tirthas. The holy tirtha associated with Kumaraswami is Kumaradhara. The Varaha Purana also mentions that Swami Pushkarni is the sporting tank of Vishnu brought down to earth from Vaikuntham. All the Puranas state conclusively that the deity on the Pushkarni is the Lord of Laxmi. Skanda came to worship Vishnu at Tirumalai. It would also be deified on Venkatachalam. The Lord's image has four arms and one face whereas Skanda should normally have six faces and twelve hands. In the verses of Nammalvar the deity is recognized clearly as Vishnu.
The image does not bear the sankha and chakra because Lord Vishnu in His infinite divine grace parted with the weapons to assist his devotee Tondaiman Chakravarti in battle against his enemies. This is confirmed in Bramhand Purana. While it is true that worship is done in the temple with bilva, it can be argued that bilva is acceptable to Lakshmi, and what is acceptable to Lakshmi is naturally acceptable to her consort, Vishnu. Vishnu images can also have jata jutas as laid down in the Bhagwata. The Nagabhushanams can not be strong arguments as Padma Purana mentions of instances of Vishnu wearing naga figures. The Bhavishyottara Purana also mentions that naga jewels were presented by Akasa Raja to his son in law and the wearing of the jewels cannot be said to be peculiar. The image of the Lord has Vakshasthala Lakshmi and also the Srivatsa mark. Even the early Alvaras who stressed the Saiva features of the image speak of him as Narayana only. The Puranas also mention that Brahma and Rudra came to worship Srinivasa when he manifested himself on Tirumalai. It is true that image has a mark on its face resembling that of crescent-moon. This however can not mean that this is a Saivite character. The image is certainly not even a Hari-Hara manifestation and is clearly a Vishnu figure." [emphasis ours]
It was Ramanuja who managed to place the weapons in the hands of the Murthi
"The Itihas Mala then states that the local ruler was fully convinced by the arguments and gave his award in favour of the Vaishnavas. Before this to put the matter beyond doubt, Ramanuja is said to have requested the king that the weapons of Vishnu and the weapons of Siva should be made and left in the temple and the matter left for finalisation by the Lord of Tirumalai Himself. Accordingly weapons of Vishnu and Siva were placed before the Lord and the temple doors closed. That night Ramanuja is said to have approached the Lord as Adishesha and prayed to the Lord to assume the Vaishnavite weapons. And lo! When the temple doors were opened next morning the Lord was found wearing the conch and the chakra! This legend from the Itihas Mala informs us that the controversy about the Hari-Hara character of the Lord existed even in the 12th century. Sri Ramanuja, himself a Srivaishnava, seems to have made up his mind to worship the Lord at Tirumalai as Lord Vishnu. The Saivite pundits of his age were certainly no match to this genius and the sage of Visitha Advaita, and there is no wonder that he won in the battle of wits, puranic lore and yogic powers and arranged for the worship of the Lord of Tirumalai from thenceforth as VISHNU" [Sitapati: 25 emphasis ours]
The image which was neglected can not be a Brahmanic one
From the above account of controversy, it is clear that Ramanuja somehow managed to get the image declared as that of Vishnu. One thing that is lost sight of is the fact that, the image must have been lying unclaimed at least for some time, before being taken up for worship by Vaishnavas or by Shaivas. This is also clearly seen from the legendary account that the image was found buried in an anthill. This legend may be taken to mean that it was neglected by original devotees, though it may not have been actually in an ant hill. There was never a time in the history of the region of Tondai Mandalam when either the Vaishnavites or the Saivites were so dormant, depressed and helpless. On the contrary it was only the Buddhists, who had to face the attacks of Saivites and Vaishnavites together. This was the reason for abandoning of the temples by the Buddhists, at various places, as already seen. There were no Buddhists left to claim the image as theirs. The very fact that the Saivites and the Vaishnavites had to fight for a neglected image, in an 'unimportant' temple, gives ample evidence that it belonged to neither of them. The arguments put forward by Ramanuja and the episode of weapons of Vishnu being taken over by the Lord Himself, might have satisfied the intelligence of Yadava Raja, but it is certainly not sufficient for people of this century.
Shaivas and Vaishnavas conspired to claim the murthi for Brahmanism
Dave, while commenting on this episode of Ramanuja managing to put weapons of Vishnu in the hands of the Lord, observes:
"Whatever the dispute, the conception of the Tirupati appears to belong to that age 'when the dominant feeling was not sectarian either Saiva or Vaishnava-but a period of compromise when sectarianism had to be kept under control because of other enemies to overcome',..." [Dave: I,117]
These 'other enemies' of course were none other than the Buddhists and Jains, as Aiyangar had observed previously in the same vein:
"The period was one in which people were making an effort to provide for worship for the masses of people, probably with a view to wean then from attachment to and attractions of other contemporary religions such as Jainism and Buddhism. It was therefore not so much of distinction, much less of antagonism, between Vaishnavism and Shaivism; but it was rather of Hinduism, kind of transformed Brahmanism as against the two heretical religions from the point of view of the Hindu..." [Aiyangar: I,195]
Thus the Vaishnavas and Shaivas, together, conspired to retain the Murthi for Brahmanic use.