I have always used the Flexible Upload plugin to upload images as it allows selection of sizes, whether to make thumbnails and choose watermarking on the upload page. Development stopped on this plugin some time ago but it has just about worked up to 3.0. Now it doesn't work at all and a couple of other upload plugins are the same. Has version 3 blocked any overriding of the upload page?
The upload page needs a watermark option and the ability to choose if an image is resized and a thumbnail made. Surely a very simple operation?
Finally the wordpress thumbnails are poor and an option to use Imagemagick to resize if it is available would be best