"Śaṅkarācārya is not at fault, for it is under the order of the Supreme Personality of Godhead that he has covered the real purport of the Vedas."
The Vedic literature is to be considered a source of real knowledge, but if one does not take it as it is, one will be misled. For example, the Bhagavad-gītā is an important Vedic literature that has been taught for many years, but because it was commented upon by unscrupulous rascals, people derived no benefit from it, and no one came to the conclusion of Kṛṣṇa consciousness. Since the purport of the Bhagavad-gītā is now being presented as it is, however, within four or five short years thousands of people all over the world have become Kṛṣṇa conscious. That is the difference between direct and indirect explanations of the Vedic literature. Therefore Śrī Caitanya Mahāprabhu said, mukhya-vṛttye sei artha parama mahattva: "To teach the Vedic literature according to its direct meaning, without false commentary, is glorious." Unfortunately, Śrī Śaṅkarācārya, by the order of the Supreme Personality of Godhead, compromised between atheism and theism in order to cheat the atheists and bring them to theism, and to do so he gave up the direct method of Vedic knowledge and tried to present a meaning which is indirect. It is with this purpose that he wrote his Śārīraka-bhāṣya commentary on the Vedānta-sūtra.

One should not, therefore, attribute very much importance to the Śārīraka-bhāṣya. In order to understand Vedānta philosophy, one must study Śrīmad-Bhāgavatam, which begins with the words oṁ namo bhagavate vāsudevāya, janmādy asya yato ’nvayād itarataś cārtheṣv abhijñaḥ sva-rāṭ: "I offer my obeisances unto Lord Śrī Kṛṣṇa, son of Vasudeva, who is the Supreme all-pervading Personality of Godhead. I meditate upon Him, the transcendent reality, who is the primeval cause of all causes, from whom all manifested universes arise, in whom they dwell and by whom they are destroyed. I meditate upon that eternally effulgent Lord, who is directly and indirectly conscious of all manifestations and yet is fully independent." (S.B.1:1:1) Śrīmad-Bhāgavatam is the real commentary on the Vedānta-sūtra. Unfortunately, if one is attracted to Śrī Śaṅkarācārya's commentary, Śārīraka-bhāṣya, his spiritual life is doomed.

(SRI CAITANYA CARITAMRTA-------1:7:110-------PURPORT).

The purpose of the discussions in the Upaniṣads and Vedānta-sūtra is to philosophically establish the personal feature of the Absolute Truth. The impersonalists, however, in order to establish their philosophy, accept these discussions in terms of lakṣaṇā-vṛtti, or indirect meanings. Thus instead of being tattva-vāda, or in search of the Absolute Truth, they become Māyāvāda, or illusioned by the material energy. When Śrī Viṣṇu Svāmī, one of the four ācāryas of the Vaiṣṇava cult, presented his thesis on the subject matter of śuddhādvaita-vāda, immediately the Māyāvādīs took advantage of this philosophy and tried to establish their advaita-vāda or kevalādvaita-vāda. To defeat this kevalādvaita-vāda, Śrī Rāmānujācārya presented his philosophy as viśiṣṭādvaita-vāda, and Śrī Madhvācārya presented his philosophy of tattva-vāda, both of which are stumbling blocks to the Māyāvādīs because they defeat their philosophy in scrupulous detail. Students of Vedic philosophy know very well how strongly Śrī Rāmānujācārya's viśiṣṭādvaita-vāda and Śrī Madhvācārya's tattva-vāda contest the impersonal Māyāvāda philosophy. Śrī Caitanya Mahāprabhu, however, accepted the direct meaning of the Vedānta philosophy and thus defeated the Māyāvāda philosophy immediately. He opined in this connection that anyone who follows the principles of the Śārīraka-bhāṣya is doomed. This is confirmed in the Padma Purāṇa, where Lord Śiva tells Pārvatī:
śṛṇu devi pravakṣyāmi tāmasāni yathā-kramam
yeṣāṁ śravaṇa-mātreṇa pātityaṁ jñāninām api
apārthaṁ śruti-vākyānāṁ darśayal loka-garhitam
karma-svarūpa-tyājyatvam atra ca pratipādyate
sarva-karma-paribhraṁśān naiṣkarmyaṁ tatra cocyate
parātma-jīvayor aikyaṁ mayātra pratipādyate

"My dear wife, hear my explanations of how I have spread ignorance through Māyāvāda philosophy. Simply by hearing it, even an advanced scholar will fall down. In this philosophy, which is certainly very inauspicious for people in general, I have misrepresented the real meaning of the Vedas and recommended that one give up all activities in order to achieve freedom from karma. In this Māyāvāda philosophy I have described the jīvātmā and Paramātmā to be one and the same." How the Māyāvāda philosophy was condemned by Śrī Caitanya Mahāprabhu and His followers is described in Śrī Caitanya-caritāmṛta, Antya-līlā, Second Chapter, verses 94 through 99, where Svarūpa-dāmodara Gosvāmī says that anyone who is eager to understand the Māyāvāda philosophy must be considered insane. This especially applies to a Vaiṣṇava who reads the Śārīraka-bhāṣya and considers himself to be one with God. The Māyāvādī philosophers have presented their arguments in such attractive, flowery language that hearing Māyāvāda philosophy may sometimes change the mind of even a mahā-bhāgavata, or very advanced devotee. An actual Vaiṣṇava cannot tolerate any philosophy that claims God and the living being to be one and the same.

(SRI CAITANYA CARITAMRTA-------1:7:110-------PURPORT).

Actually in the first two chapters of Vedānta-sūtra the relationship between the living entities and the Supreme Lord is explained, and in the Third Chapter the discharge of devotional service is explained. The Fourth Chapter deals with the relationship which results from discharging devotional service. The natural commentary on Vedānta-sūtra is Śrīmad-Bhāgavatam. The great ācāryas of the four Vaiṣṇava communities (sampradāyas)—namely, Rāmānujācārya, Madhvācārya, Viṣṇu Svāmī and Nimbārka—have also written commentaries on Vedānta-sūtra by following the principles of Śrīmad-Bhāgavatam. At present the followers of all the ācāryas have written many books following the principles of Śrīmad-Bhāgavatam as the commentary on the Vedānta. Śaṅkara's commentary on Vedānta-sūtra, known as Śārīraka-bhāṣya, is very much adored by the impersonalist scholars, but commentaries written on the Vedānta written from the materialistic point of view are completely adverse to the transcendental service of the Lord. Consequently Lord Caitanya said that direct commentaries on the Upaniṣads and Vedānta-sūtra are glorious, but that anyone who follows the indirect path of Śaṅkarācārya's Śārīraka-bhāṣya is certainly doomed.
Lord Caitanya admitted that Śaṅkarācārya was an incarnation of Lord Śiva, and it is known that Lord Śiva is one of the greatest devotees (a mahājana) of the Bhāgavata school. There are twelve great authorities on devotional service, and Lord Śiva is one of them. Why, then, did he adopt the process of Māyāvādī philosophy? The answer is given in Padma Purāṇa, where Lord Śiva states:

māyāvādam asac-chāstraṁ
pracchannaṁ bauddham ucyate
mayaiva kalpitaṁ devi
kalau brāhmaṇa-rūpiṇā
"The Māyāvādī philosophy is veiled Buddhism." In other words, the voidist philosophy of Buddha is more or less repeated in the Māyāvādī philosophy of impersonalism, although the Māyāvādī philosophy claims to be directed by the Vedic conclusions. Lord Śiva, however, admits that this philosophy is manufactured by him in the age of Kali in order to mislead the atheists. "Actually the Supreme Personality of Godhead has His transcendental body," Lord Śiva states. "But I describe the Supreme as impersonal. I also explain the Vedānta-sūtra according to the same principles of Māyāvādī philosophy."

In the Śiva Purāṇa the Supreme Lord says:

dvāparādau yuge bhūtvā
kalayā mānuṣādiṣu
svāgamaiḥ kalpitais tvaṁ ca
janān mad-vimukhān kuru
"In the beginning of the Dvāpara-yuga, directed by My orders, many sages will bewilder the people in general by Māyāvādī philosophy." In the Padma Purāṇa Lord Śiva personally tells Bhāgavatīdevī:

śṛṇu devi parakṣyāmi
tāmasāni yathā-kramam
yeṣāṁ śravaṇa-mātreṇa
pātityaṁ jñāninām api
apārthaṁ śruti-vākyānāṁ
darśayaḻ loka-garhitam
karma-svarūpa-tyājyatvam
atra ca pratipādyate
sarva-karma-paribhraṁśān
naiskarmyaṁ tatra cocyate
parātma jīvayor aikyaṁ
mayātra pratipādyate
"My dear Devī, sometimes I teach Māyāvādī philosophy for those who are engrossed in the mode of ignorance. But if a person in the mode of goodness happens to hear this Māyāvādī philosophy, he falls down, for when teaching Māyāvādī philosophy, I say that the living entity and the Supreme Lord are one and the same."

(TEACHINGS OF LORD CAITANYA).

Śrī Caitanya Mahāprabhu presented Himself as if He were a sannyāsī in name only or, in other words, a number-one fool. Māyāvādī sannyāsīs in India are very much accustomed to declaring themselves jagad-gurus, teachers of the world, although they have no information of the outside world and are limited in their experience to a small town or village, or perhaps to the country of India. Nor do such sannyāsīs have sufficient education. Unfortunately, at the present moment there are many foolish sannyāsīs, both in India and elsewhere, who simply read and study Vedic literature without understanding the purports. When Caitanya Mahāprabhu was having His discussion with the Chand Kazi, the Muslim magistrate of Navadvīpa, He recited a verse from the Vedic literature to the effect that the order of sannyāsa is prohibited in this Age of Kali. Only those who are very serious and who follow the regulative principles and study Vedic literature should accept sannyāsa. Śrī Caitanya Mahāprabhu approved of a sannyāsī’s reading the Vedānta-sūtra, or Brahma-sūtra, but He did not approve the Śārīraka commentary of Śaṅkarācārya. Indeed, He said elsewhere, māyāvādi-bhāṣya śunile haya sarva-nāśa: (CC.2:6:169) "If one hears the Śārīraka-bhāṣya of Śaṅkarācārya, he is doomed." Thus a sannyāsī, a transcendentalist, must read the Vedānta-sūtra regularly, but he should not read the Śārīraka-bhāṣya. This is the conclusion of Śrī Caitanya Mahāprabhu. The real commentary on the Vedānta-sūtra is Śrīmad-Bhāgavatam. Artho ’yaṁ brahma-sūtrānām: Śrīmad-Bhāgavatam is the original commentary on the Vedānta-sūtra, written by the author himself, Śrīla Vyāsadeva.

(SRI CAITANYA CARITAMRTA-------2:6:127-------PURPORT).