First of all this is an EXCELLENT plugin. Clean and fast.
Some limitations i found are:
1. All images are in the default WP media folder and that can be very very confusing. And messy if you have many photos. Each gallery / album should have a directory (and be removed when uninstalled).
2. No paging in the albums ! If you have 1000 images, you have 1000 thumbs in one page. This can bring the hosting plan down and create some slow galleries/albums
3. Some formating options should be available. For example how many photos per ROW or the option to show the photos description or title.
Again, i'm shocked on how well this plugin is done. I have uploaded all kind of strange dimensions photos and the plugin handles it very very well (Panoramics for example).