In a new essay, Richard Bauckham rejects the sacramental interpretation of Jn 3 & 6: "Sacraments?," Gospel of Glory: Major Themes in Johannine Theology (Baker 2015), chap. 5.
To summarize some key details in his argument:
i) He rejects the baptismal interpretation of Jn 3 in part because that's anachronistic. Indeed, he quotes scholars who support the baptismal interpretation, but admit that it's anachronistic:
[Raymond Brown] If we posit some kind of historical tradition behind the Nicodemus incident, then we must allow a primary nonsacramental meaning to Jesus's words, a meaning which Nicodemus could have understood. Ibid. 82n24.
Ignace de la Potterie maintains a primary reference to Christian baptism that does not have to be intelligible to Nicodemus because the author of the Gospel added the words "water and" only at a later stage of composition. Ibid. 84n33.
ii) For scholars like Brown, they don't think the historical anachronism is problematic because they don't think the conversation ever took place. For them, it's a retrojection. A fictional dialogue.
However, Bauckham thinks that's mistaken even if you deny the historicity of the account. For even if it's fictional, it was still meant to be realistic:
A plausible interpretation must make sense in its narrative context, which is Jesus's conversation with Nicodemus, a Pharisaic member of the Jewish ruling council, in Jerusalem at an early stage of Jesus's earthly ministry. This criterion should not be confused with the assumption that the narrative is a historical report of a conversation that actually took place. Even if the narrative is entirely fictional, the criterion applies because it is entailed by the literary genre of the text as a narrative set in the past. Ibid. 82-83.
Although I disagree with the fictional classification, this is a way of rebutting liberal scholars on their own grounds.
iii) Bauckham argues that the "water" is a reference to amniotic fluid. This picks on up Nicodemus's reference to childbirth, then builds on that to create a parallel. Everyone who enters the kingdom must be twice-born: naturally born and spiritually reborn. Born of the flesh and born of the Spirit.
iv) Concerning Jn 6, he argues that Isa 54:9-55:5 function as a key interpretive filter:
As well as the explicit quotation (v45=Isa 54:13), there are a series of allusions to Isa 55:1-3 ("thirst…come…eat…bread…come to me…so that you may live") in vv 35,37,40,44,45,47,51,54,57,58.
Jesus here identifies himself not only with the bread of the Exodus text, but also with the divine speaker in Isa 55, who offers both food and drink to those who come to him…When Jesus says that "my flesh is true food and my blood is true drink," there is probably an allusion to Isa 55:2, where "that which is not bread" and "that which does not satisfy" are contrasted with the food and drink that God gives. Ibid. 96.
iv) Although he rejects the eucharistic interpretation of Jn 6, Bauckam thinks the discourse employs some eucharistic language to explicate the sacrificial import of Christ's impending death. The eucharist is, itself, an interpretation of the cross, which unpacks the death of Christ in sacrificial terms (i.e. to atone for sin). Bauckham thinks that Jn 6 trades on eucharistic connotations, even though it is not, in itself, eucharistic.
However, Bauckham admits that in OT sacrificial system, "flesh" and "blood" terminology was used (e.g. Lev 1:3-9). So eucharistic allusions are unnecessary to evoke the sacramental significance of Jesus' impending death in Jn 6.