I do think even in J2 fics it's possible to write them in character or not.
I agree that there are definitely certain characteristics that are consistent across many fics -- but not all fics. There are a couple of examples that come to mind where J&J could have been replaced by original characters and I wouldn't have even known the difference -- I've enjoyed said fics, but we all have different characterizations of J&J in our own minds and some people have a more defined view of J&J while others have a much looser view (i.e. a wider range of behaviours are accepted as Jensen-like or Jared-like), which is probably why the search+replace strategy works for some people (I've never actually tried it myself, so I can't say if it would work for me ^__^;;).
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I agree that there are definitely certain characteristics that are consistent across many fics -- but not all fics. There are a couple of examples that come to mind where J&J could have been replaced by original characters and I wouldn't have even known the difference -- I've enjoyed said fics, but we all have different characterizations of J&J in our own minds and some people have a more defined view of J&J while others have a much looser view (i.e. a wider range of behaviours are accepted as Jensen-like or Jared-like), which is probably why the search+replace strategy works for some people (I've never actually tried it myself, so I can't say if it would work for me ^__^;;).