In his explanation for the nAma catur-vyUha in his vyAkhyAnam of SrI vishNu sahasra nAmam, SrI Sankara has given a reference to mahA-bhArata supporting the vyuha concept. The vyUha concept is an integral part of the pA~ncarAtra doctrine. It is known that SrI Sankara had opposed the pA~ncarAtra Agama, and this was part of the reason that contributed to the questioning of the pA~ncaratra system in his time and the immediately following period.
Based on the bhAshya for brahma sutra by SrI Sankara, it is evident that SrI Sankara does not accept the pAncarAtra doctrine. However, there are certain aspects of the pAncarAtra doctrine with which he agrees. vyuha, or the division of the supreme Brahman into many forms, is one aspect that he accepts. In his preface to a book on pAdma samhitA, sudarSanam SrI Kr*shNasvAmi aiyangAr has included a section of the original samskr*t commentary by SrI Sankara for the brahma sutra II.2.42 - which clarifies this.
"tatra yat-tAvaducyate yo'sau nArAyaNah paro'vyaktAt prasiddhah paramAtmA sa AtmanAtmAnam anekadhA vyuha avasthita iti, tat na nirAkriyate. (Note the words 'na nirAkriyate). 'sa ekadhA bhavati, tridhA bhavati' (chAndogya 7.26.2) ityAdi Srutibhyah paramAtmanah anekadhA bhAvasya adhigatatvAt. yadapi tasya bhagavatah abhigamanAdi lakshNam ArAdhanam ajasram ananya cittatayA abhipreyate tadapi na pratishidhyate (again, note the words na pratishidhyate). Sruti-smr*tyoh esvara-praNidhAnasya prasiddhatvAt.
The translation of the above words of SrI Sankara is "We do not refute the view stated therein that nArAyaNa, who is superior to Nature and who is well-known to be the supreme Self and the Self of all, has divided Himself by Himself into many forms; for from vedic texts such as - He assumes one form, He assumes three forms etc., it is known that the Supreme Self does become multifarious. As for the predilection for His propitiation, consisting in visiting His temple etc., and so on, with exclusive devotion and for long, that also is not denied. For the contemplation of God is well in evidence in the veda-s and smr*ti-s." - translation is taken from svAmi gambhIrAnanda, advaita ASrama publication.
The major objection SrI Sankara has for the pAncarAtra system is on how the beings called sankarshaNa, pradyumna, and aniruddha resulted from the supreme Self, vAsudeva. It is very interesting to read the vyAkhyYna-s of SrI Sankara and SrI rAmAnuja for the sutra-s "utpatti asambhavAt, na ca kartuh karaNam, vij~nAnAdi bhAve vA tat apratishedhah, and vipratishedAcca, wherein the objections are raised and answered. Briefly, SrI Sankara's objections are - a) The soul called sankarshaNa could not have originated from the Self vAsudeva, since a soul cannot be born or created according to veda-s; b) If vAsudeva, sankarshaNa, pradyumna, and aniruddha are all of equal knowledge, powers, etc., as the bhAgavata doctrine maintains, there is no need for four forms, since one form could have carried out all the functions of the God; c) If they are of all of equal knowledge and powers etc., then one could not have originated from another, since the cause and effect should have some difference in order to differentiate them, and yet the bhAgavata-s insist that there are not different.
SrI rAmAnuja points out that the origin of sankarshaNa from vAsudeva etc. in this context should be viewed as the voluntary assumption of bodily forms by the supreme Brahman vAsudeva out of compassion for its devotees, so that the devotees can have easy access to the supreme Brahman. This is because vAsudeva the supreme Brahman has for its body the pure aggregate of the six supreme qualities, and thus is difficult for all to attain easily. The devotee attains to the vyuha forms by worshipping the vibhava forms such as worship of rAma, kr*shna, etc., and from the vyuha forms he attains to the Subtle form of vAsudeva. If birth or origination of sankarshaNa from vAsudeva etc. is viewed thus, there is no contradiction between the pAncarAtra doctrine and the veda-s. In fact, the pAncarAtra doctrine is considered to include in it all the other veda-s, the sAnkhya-yoga, and AraNyaka-s.
Thus, in summary, while it is true that SrI Sankara did not accept the pAncarAtra doctrine in its enitrety because he had issues with certain aspects of it, by his own words, there are certain aspects of the pAncarAtra doctrine that he also agreed with, e.g., vAsudeva as the supreme Brahman, its ability to divide itself and manifest itself in many forms, dedicated worship to vAsudeva in temples, etc.