Adding to the answers given before I'd like to mention the following:
From the theoretical point of view Guitar tuning is much more complicated than piano tuning. Or in other words: It is more a compromise than tuning a keyboard instrument, as you have to consider each fret separately and simultaniously for all strings. This may be the reason that the 12-tone equal tempered tuning (short 12-tet) has been first reported in the wester music tradition as the solution to the problem of lute division.
As a secound point is related to just intonation. You can express the sound of one string by different frequencies. As a good approximation you can consider the inner ear as a gammatone filter bank with 3000 to 4000 frequencies, a Fourier series is often resonable, too. A just fifth/fourth as the difference between g and d is not very robust against mistuning. According to some authors (e.g. Martin Vogel) the just noticable difference of two sine tones (about 1-2ct) is also noticable in the timbre of two strings tuned a fifth apart when played together. This explains why the two strings interact with each other.
The third thing is related to the aging process you are referring to: The natural learning curve is not linear. At the beginning you are lerning to understand the problem. This is the first noticable phase of learning. Later on you learn from variation. This means that you do not notice any progress. I assume that you try to avoid variation in the tuning result. So collectiong variation might be difficult and a long process. After you collected enough variation there may be the point where you suddenly reach a new quality of your task – in this case the listening to the tuning of your guitar.
Finally I'd like come back to the physical behaviour of your guitar. Preferably the corpus has no undamped resonance frequency. I own a guitar which has a relatively strong weakly damped resonance frequency, which makes it hard to tune a particular string. Depending on your hearnig skills you may even notice the difference in the degree of different partials of your guitar strings. Sometimes these can be caused by the strings themselves (e.g. nylon strings may loose homogeneity over time).
As a conclusion your description sounds to me as if you somehow got another instrument, your instrument needs some maintenance (e.g. new strings), or you improved your hearings skills over time. It might be also a combination of these things.