Hmm...
There are actually minute differences in every major key precisely because of the equal temperament tuning system.
Yes, if you play a major scale in any key, it will be recognized as a major scale. This is of course correct because of the order steps that creates a major scale (WWHWWWH).
BUT...
The equal temperament system was created to make keys based off of all notes sound as similar as possible. It is impossible, however, to create a perfectly in tune scale on every key if you're using static tuned strings or a stringed instruments with frets. The physics of sound prohibit this. You may create a perfect scale for the key of C on a piano, and tune the strings accordingly, but then as soon as you start playing a B major scale, or an A major scale, things will sound noticeably off. For this reason, there ARE minute differences in the way that different keys sound. A major scale on a piano, no matter what scale you play, will always be a bit out of tune relative to a PERFECT major scale, but only slightly so.
Now, of course, as I said before, every scale you play on a piano will sound like the same scale in a different key, but there will be subtle differences. This is why if you try to tune your guitar completely by ear or by absolutely perfect fifths, it will sound more out of tune in some keys than in others.
So experiment with your tune in differenct keys, it may actually sound better/more interesting in one key as opposed to another. The subtle differences in the consonance and dissonance created between scale degrees may make your tune work better in certain keys.
As far as the benifit of learning to play in all keys, there is the obvious benifit of being able to modulate through the cycle of fifths (or fourths).
Modulation is a great technique for getting your tunes to sound original. Why use only one major key or minor key in your tune, when you have tons of other keys to choose from?
Dude.