Why is __FILE__ uppercase and __dir__ lowercase?

I think that is because __FILE__ is a parse-time constant whereas __dir__ is a function and returns File.dirname(File.realpath(__FILE__))

For more details, see This discussion

TL; DR

The relative merits of language implementation choices are outside the scope of a reasonable Stack Overflow question. However, this is a good question because it identifies a potentially confusing use case in the language and seeks to clarify the distinction between the two language elements.

Keywords, Methods, and Keywords That Look Like Methods

__FILE__ is a Keyword

In Ruby 1.9, __FILE__ is a keyword. Even though it looks like a method defined on the Object class, the source for Object#__FILE__ says:

# File keywords.rb, line 68
def __FILE__
end

A quick scan of the source in 2.0.0-p0 didn't turn up a keywords.rb file, but one assumes that __FILE__ syntactically remains a keyword. Perhaps someone else can point you to the location of the current definition.

__dir__ is a Method

Kernel#__dir__ is actually a method. You can see this for yourself by grepping the Kernel's defined methods:

Kernel.methods.grep /__dir__/
# => [:__dir__]

Bugs and Discussions

The fact that __FILE__ is both a keyword and (sort of) a method is called out in a bug and some bug-related commentary. There was also discussion of the various pros and cons of the naming convention in the Ruby-Core Forum.

While the answer may be a bit unsatisfactory, that's the current state of affairs. If it's a language design issue you feel strongly about, getting involved with the Ruby core team would be the proper way to address it.