See this thread too:
http://www.japanesepod101.com/forum/vie ... 0333#10333
I do not think the pdf format is good, you can't use any pop up dictionaries. 
How about .html instead?
Words in the hiragana transcription should be written with spaces between them.
The text, the trascription and the translation should all be placed side by side in VERTICAL parallel columns. It is much easier to find the meaning.
Sentences in GRAMMAR BANK sould be recorded as well, learning a language without audio is a source of hell of a lot of mistakes.
And instead of senteces short dialogues are much better.
And why not recording, let's say fifty or at least twenty differnt verbs and i-adjectives, all of them conjugated in as many forms as possible?
And less English in the recordins to download, all in Japanese but with transcripts and translations.
What about some longer stories?
And some jokes, sex, and poetry?
And a new section on pronunciation (moras, TONES) would be much appreciated. 
I know it means much more work, but ......
After all life is too short to waste it on trifles, I mean short dialogues about nothing in particular.
By the way, yours is probly the best site out there for learners of Japanese (I've seen hundreds of them in many languages), but it is still too traditional.
							 
                                             there's nothing unnecessary, it reaches where others don't . It's the only one which do a lot of grammar, that has kanji sheets, that has nice voice actors. Yes maybe it could be better but I do not see anything traditional that it's not necessary! These are lesson that are made to be listened to by an MP3 player, you cannot make them too long or complicated!!!
  there's nothing unnecessary, it reaches where others don't . It's the only one which do a lot of grammar, that has kanji sheets, that has nice voice actors. Yes maybe it could be better but I do not see anything traditional that it's not necessary! These are lesson that are made to be listened to by an MP3 player, you cannot make them too long or complicated!!!