This is going to sound waaaay out of left field...
I think the biggest problem with all of these information managers is none of them offer the user a good way to customize how they want to SEE the information. Look, storing information is easy. Even without any special programs, it's easy to just use a good file manager to organize a bunch of files and folders. What a lot of these programs do is focus on the STORAGE of information, which to me is not a big deal. That's why i always struggle with that part. I'm fine with basic file management, I don't need a new way to manage files.
The presentation is where it gets bad. All of these programs either want you to view your data in THEIR way, which usually only resonates with a specific group of people. But you don't have the ability to tweak it to what you need. Just to prove my point further, most of these information managers have really awful printing support. Most of them are very basic, maybe the default IE type print preview thing.
The reason why this is bad is because why am I going to spend all this time importing/creating the database, if I'm not going to see or get out the end result of what I want?
Which is why I think my ultimate idea for a program like this would be awesome, but I don't have the talent to create it:
The ultimate information management program:
First, it should be able to import content in easily. Especially content that is "very normal". text files, ms office files, pictures, popular database formats. That takes care of bringing things in.
Then, it should offer a flexible way to establish relationships among all these items. Hierarchies should be easy to make, like in infoqube, ecco pro. Hierarchies are essential. I don't care if you call it tagging or outlining, but relating content needs to be easy.
Now for the best part. I should be able to take all these content elements and like a desktop publishing program, specify how they should be laid out and so forth. So I can print it, export it to an image or html file, etc. This is what most programs lack big time.
Once you like a certain layout, you should be able to save that layout as a template or something and reuse it easily with other data.
That's an idea worth exploring, I think. We spend too much time designing how to bring content into the application. There are tons of programs that do this. Any program like MS Word is going to be better at writing stuff than an information manager, yet they all go through the whole exercise of giving us a Word-lite editor, that people keep requesting more features to make it more like Word. Then they don't have this feature or that feature, like image resizing, rotating, etc...but all this stuff is done better with programs specific for that. This is what most developers spend their time doing.
What is consistently neglected: printing features, export/import features, interface improvements. No. we keep doing the same mistake everyone else in this world does: make it bigger, bigger, more stuff, more stuff...yet never go back and fine-tune or fix things that we have now had a chance to use and improve. Just like google, it used to be awesome, now there's so much crap on it that it's 99% crap, 1% useful. So you might argue it's still worth it for that 1%, but after a while, you give up because your tired...you're tired of wading through all the crap to find that one thing.
I'm on a big fix with elegance lately, since I see so little of it in my life. granted, I'm an engineer in los Angeles (how ugly and boring can it get?!) but I still see very few examples of it around. Plus, I'm super cynical now.