Well, using that logic, I guess you could make the claim that you could use Evernote in place of Word, Notepad, or really any application that is note/text editing related. But I think that most do not wish to do so, or the other journal/text editing/note-taking programs would be out of business!
The features that many look for are one's more specific to their needs, rather than taking generic applications and force-fitting them to do all.
Just my opinion.
I agree (at least... partly) with you.
But I'm not really comparing EverNote or The journal to MS word (even though I might have given that impression earlier).
And I'm comparing EverNote to the Journal because it actually does everything I want for a Journal.
Like said earlier, I like the fact that my text can be indexed with the Desktop Search software I use. This is the main reason why I brought MS Word in the picture (put it could be OpenOffice, or WordPad, or Even OneNote : if it's indexable...).
Also, too many apps for different, yet not that different, tasks, makes my life much more complicated: different formats, data scattered in different places, etc. Using the GTD approach, I try to centralize the way I gather data as much as I can.
But I can see why one would do that, and I totally respect that. I'm just too absent minded -- which is not very convenient when you're trying to write a thesis (don't worry, I'm not writing it in English!).