I do not use much of the software Apple gives with its computers but I do learn it anyways. I find it handy for quick, simple little things I need to get done. Like lowering the file size of a PDF with Preview. Doing a quick 10 or 15 second video clip with iMovie, Garageband or iPhoto. The Help Menus in each program are such a good feature. I have Adobe for the larger work load.
The programs will only frustrate you if you let them. Yes Apple has dumbed down some of their programs to far, such as the new iWork suite, but at least they are not overwriting all the old programs with the new ones, which means you still have the old ones to work with. That is not with all the programs but at least some of them.
You have other alternatives out there to choose from. I was not totally happy with Finder and wanted more features so I purchased TotalFinder. Wanted more feature for my dock so I purchased HyperDock. And so on. As you stated, you wanted more photo editing feature than iPhoto could offer so you went with Pixelmator. Good coice by the way and cheap.
Yes I know, here I am saying spend more money, but if you want added features, someone has to be paid for their time to create them. And most times when you buy a program or plugin to add features you end up with more than you need. Which can be a bonus in the end.
Considering the software comes free from Apple it does a pretty good job in most cases and a lot of people are using it without issues.