Trains are something Anno likes.Evangelion
is itself an exploration of his issues through a medium he enjoys, and he draws upon his other interests several times in the series. The naval ships in episode 8, the aircraft which carry the Eva's that wouldn't be out of place in a Shigeru Komatsuzaki drawing, the entire naming convention of the characters, etc.
That isn't to say that there wasn't something behind the usage of trains. Theta state
thinking tends to happen in moments of calm, when our bodies are at rest or are somehow occupied. Equally, Evangelion
is itself a highly cerebral work, predicated on the inner thoughts of the creator.
As such, it's plausible Hideaki Anno himself had many of his owns fits and breakthroughs while sitting on a train, and came to associate the aesthetic experience of it with a certain mindset.
This might in fact explain the discrepancy in portrayal; maglev's are cool and Evangelion
, at least in establishing its setting, likes to embrace cool. But without the clickety-clack
it's also less real, less the atmosphere Anno is trying to recapture on film.