A great plugin that works for both cases, i.e. with custom post type gallery management and also with default wp gallery shortcodes!!
(Using gpp slideshow 1.3.1 with wp 3.5.1)
Two things are there required...
As the plugin describes it does not resize the images in slideshow.
For the inbuilt wp gallery usage case, I think there should be additional parameter in gallery shortcode that if included like [gallery link="file" ids="79,104,105" size="600x400"] or [gallery ids="79,104,105" width="600" height="400"] , then it will be best. If not included then there should be default behavior as current. In my case, I have many images in media gallery that I select from different post galleries. So, its not possible and easy to check the width height of each and every images or if not found upload the same image again with required size.
Also, not good if same image may be need to use at different place may be inside a post with different size.
If using without exact size upload, the different size image when chosen making all extra area blank for smaller image in frontend slideshow as its occupying space for largest image, but caption, top thumbnails etc. seems outside when smaller image active.
Second thing, (via wp gallery shortcode usage) this plugin if activated converts all galleries to gpp slideshow, but what if I want to use some galleries as slideshow and some as default wp gallery? For this, there should be an additional shortcode like [gallery link="file" ids="79,104,105" nogpp] . This argument 'nogpp' can help to identify that this gallery not to be gpp-slideshow and work as default wp.
It can be set as a shortcode as I have given in examples or via additional custom fields in admin media panel while creating gallery, as this plugin do.. see http://wordpress.org/extend/plugins/wp-gallery-custom-links/ . This plugin extend the inbuilt gallery but override the custom links with additional fields even for each single image in a gallery.
In gpp this not needed upto image level, but control can be added upto gallery level for size and no-gpp solution.
These are like feature requests but are very obvious needs for users. I hope you to include this in next release soon, will make this plugin more popular and usable.