Wise Turtle Publishing

While spending experience for raising Abilities is mentioned on p. 87, the chapter doesn't say anything about how to lower / remove a Weakness with Experience Points. (It mentions removing them later as a result of "interactions with the world").
So what would be an appropriate amount for removing a Weakness? The negative amount in EP? Like, 2 EP to get from -2 to -1?

There's a reason this is not listed. While Abilities can be conceivably be improved or learned between adventures, Weaknesses are far less easy to get rid of and should require investment with both role-playing and time. Buying off Weaknesses makes no logical sense, and really, is too easy.

If you MUST, yes, your suggestion seems all right.

Clay wrote:While Abilities can be conceivably be improved or learned between adventures, Weaknesses are far less easy to get rid of and should require investment with both role-playing and time.

I think there is not actual difference between Abilities & Weaknesses in this regard. The problem arises from the Experience Point system itself. Dealing out XP for actions that don't have a direct connection to the story itself ("Be there", "Be Involved") is fine as it encourages role-playing, but doesn't answer the question on what you can/should spend these XP.
You already mention the solution: The GM may allow to spend the player XP on skills, Abilities (and Weaknesses) if there is a justification in the story.

Miho should be allowed to improve her Ineptitude in Cooking (but I'd prefer if the player wouldn't do that as it is such an amusing cliché).
A character working out heavily should be allowed going from Strong +1 to Strong +2 as well as from Weak -2 to Weak -1.
On the other hand, the only thing Fukiko can do to improve her Frail -2 is to grow up
Removing negative character (Arrogant, Boorish, Compulsion etc) should be role-played well before allowing the player to spent XP.

The basic idea here is that you can gain Abilities and lose Weaknesses, effectively, free through role-playing. All EXP is for is a little extra bonus, a reward for playing. Anything more than minor improvements is not terribly practical.

I wanted the focus to remain on role-playing. That's why EXP is hampered in what it can do. If I felt I could've gotten away with it, there'd be no EXP at all. But I thought that might be TOO alienating to long time RPers.

And EXP is always a fun bonus.

Yeah, we all need that XP measuring stick. I wish I was more attentive. I thought you could just buy off weaknesses with XP like momosnyx suggested by default. my bad.

You can, now. The post you found was quite old and referenced the first edition rules. The Revised game allows you to do just that (but encourages you to try role-playing it out instead.)