Paul said "Christ sent me not to baptize, but to preach the Gospel". (1 Cor 1:17). Yes he baptised a couple of people, however note how he also says he is glad he didn't baptise any others. Most importantly, those that he did baptise were Jews, so their baptism was in keeping with the way in which early converts from Judaism kept their Jewish traditions. Paul did it for the same reason he had Timothy circumcised... so that he might be a Jew to the Jews, and a Gentile to the Gentiles. We don't give that as proof that Christians ought to be circumcised, so why do it with baptism?
Also I think John 3:5 is symbolism, again looking to the example of Hebrews... the idea of the living water and never thirsting again.
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