I own a T3i with the kit lens. I have experimented a lot with different settings and modes but I am not so knowledgeable and I feel like I have wasted many good shots that could have looked amazing, if only they were a little bit sharper.

I use Auto-Focus on most of my pictures and I make sure I choose the right focus point

Take for example this photo (It is a little bit out of focus, which is true for all of my photos):

https://www.flickr.com/photos/105969533@N05/14105361962/

If you download it and zoom in, you can see the pixels are not very crisp and well-aligned. Please ask for any clarification you might need: I have many photos to make my point.

I am not sure if this issue is caused by my equipment or skills.