From an aesthetic point of view, the App Store is just plain ugly. Even when opening further, it takes work to find out what the program is intended to do, and there are no links to discover other programs that work in the same area so I can compare them. Amazon does this better, and I can enlarge their text and make it readable.
Pages is an example of a bad program. They are so interested in what their graphics can do that they miss the point of a word processor completely. I highly recommend getting MacTex or TexShop or whatever form of Latex you prefer directly from their website (see complaints about App Store above, and beware), installing it, buying LaTeX: Line by Line and finding out that you can write excellent, good looking letters, articles, monographs and books with very little trouble. There are free Latex tutorials out there, too, if you'd prefer. TexShop will let me enlarge the text to any reasonable size on the screen to work with, and handle footnotes, bibliography &c. with aplomb. It's not a cute program, just one that produces beautiful output.
Contacts, the program for addresses and phone numbers, is dramatically less useful than a flat text file with search and replace. Not only does it create the screen rectangle, it is not set up for the kind of address and phone access that I need: one that lets me say, "444-8765, whose number was that?" and pop up the possibilities.
The mail program I disabled for the same reason: ugly, hard to make legible, and generally too stubborn to handle the screen. Possibly these would look better on a small screen where I have no choice but to have a magnifying glass beside the screen, but I don't think that's the way to design.
iphoto doesn't search the disk for photos, you have to find and add the appropriate folders yourself.
There are lots of upsides. The one that sold me originally was that it wasn't Microsoft: after having dealt with them since the IBMPC Model 1 (complete with tape drive socket for backups) DOS 1.1, they finally lost me last year by making my recent PC a brick with a surprise Windows re-authorization (I was on the phone and computer with them at the time. It was them, not me.) In comparison, Apple has handled issues well.