So I'm busy generating and tallying up scores for offered pokemon in a trade, here's how it stands now:
1) Each pokemon in an offer has its encounter rate inverted from 100. So for example, a 75% encounter rate zubat leaves only 25 as a base starting score.
2) The score is then doubled, just to push differences apart further.
3) If the pokemon is version limited, it gets another 50 added to its score.
4) If the pokemon is shiny, its score is multiplied by an arbitrarily chosen 12.5x.
Each pokemon in a trade can be hovered over to see its score. So at the end of this, a pidgeot is worth 90, a gardevoir 140, a charmeleon 120. A shiny charmeleon is worth 1,500.
Of course, much of the value from trading is sentimental, friendship based or some other reason that means the actual rarity of the pokemon is irrelevant. So it's just a little number in the corner, and each pokemon's individual score is hidden until you hover over its name. Just helps at a glance if you're wondering how rare the particular pokemon is. Also, pokemon in a trade now link to their info pages.
And there's now a link to IRC when in a trade