Music only settled on 12 equal tones after a lot of music theory and a lot of compromise. Early instruments often picked a scale and stuck with it, and even if they could produce different scales, early music stuck to a single scale without accidentals for long stretches. Many of these only had 5 or 6 notes, but at the time and place these names were settling down, 7-note scales were common, so we have the 8th note being the doubling of the 1st.
Most beginners still start out thinking in one scale at a time (except perhaps Guitar, which sorta has its own system that's more efficient for playing basic rock). So thinking about music as having 7 notes over a base "tonic" note, plus some allowed modifications to those notes, is still a very useful model.
The problem is that these names percolated down to the intervals. It is silly that a "second" is an interval of length 1. One octave is an 8th, but two octaves is a 15th. Very annoying. However, it still makes sense to number them based on the scale, rather than half-steps: every scale contains one of every interval over the tonic, and you have a few choices, like "minor thirds vs. major thirds" (or what should be "minor seconds vs. major seconds"). It's a lot less obvious that you should* only include either a "fourth" (minor 3rd) or a "fifth" (major 3rd), but not both. I think we got here because we started by referring to notes by where they appear in the scale ("the third note"), and only later started thinking more in terms of intervals, and we wanted "a third over the tonic" to be the same as the third note in the scale. In this case it would have been nice if both started at zero, but that would have been amazing foresight from early music theorists.
* Of course you can do whatever you want -- if it sounds good, do it. But most of the point of these terms (and music theory in general) is communicating with other musicians. Musicians think in scales because not doing so generally just does not sound good. If your song uses a scale that includes both the minor and major third, that's an unusual choice, and unusual choices requiring unusual syntax is a good thing, as it highlights it to other musicians.