Thumbnails is a light plugin which helps your theme to generate thumbnails. Most of the thumbnails can be generated on the fly and stored in a cache folder, instead to full fill your upload folder. More, you change theme and the thumbs sizes changes you can be in trouble with old images.
With Thumbnails there is no more problems.
The new feature are the persistent autowired featured image which really improve the performances of the older versions and the ability to process images for the core sizes (limited to the thumbnail size of WordPress).