| Chords are one big reason. Another, somewhat related, reason has to do with the question of which notes you're likely to use in a given key or at a given position, and of which notes you have available to you as open strings. For instance, if you're playing in E minor (for which the 5th is B), having a high open B and a high open E available is probably going to be more use to you than having a high C and F. If you capo up to the 3rd and play in G, the high D and G are going to be more useful than a high Eb and Ab. If you're playing in, say, 6th position in the key of Bb, it's handy that your low F (on a 5 string) is also on the 6th fret; on a BEADGB or EADGBE bass, *your high F is also at the 6th position,* so you don't have to shift to get it.
Historically, having this little irregularity in the intervals between the strings is not an exception but is in fact more like the rule, at least in Western music of the past few centuries. Really, it's the 6 string electric bass, as it's usually tuned, that's the freak here. Not that that's inhehently either good or bad, of course.
Another possible reason, which would operate probably more for acoustic guitars than for basses, would be sympathetic resonances. Hit a low E, and the high E is gonna resonate with it; a high F won't.
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B1500 Club #18
ABG Club #89
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