I did run into one issue, when using slim box as the popup method, the popup appears behind my upper menu system. (rocket theme template) There was one post here describing that issue and what they did in the CSS to solve it, but I didn't understand the code they were describing. (I'm not a coder).
But on most templates, it works great, and even in my case the other "modes" of the popup, work fine. Also, there is an option that the thumbnail will take you to the article when in 'blog mode' instead of doing the popup. (once you are in the article, the thumbnails then popup to a larger size)
The other other change I would suggest, is a simple button in the plugin setup that will purge the no longer used thumbnails from the system, they do accumulate in there. If you experiment when placing an image, and try 3 or 4 different sizes, then decide on 1... the old thumbnails that were generated during testing still exist in the server. This doesn't hurt anything, but does take up space.