The 2 tables are left there intentionally. They are used in all vBa products, and leaving them there after an uninstall won't affect anything.
The indexes I really have no clue about right now. As long as you followed through the steps in the uninstall and it said they were removed, then they should be. Of course you can always run some manual queries to drop them though.
For the phrases, it looks like there might be a small bug in the install file that's preventing them from being removed. Of course you can run a query to drop all phrases with 'adv_cmps' as the product. Or, look in the install file for this code:
Replace with this:
And that should fix that problem.
As for the 13 templates, the ones you listed are default vBulletin templates used for your image paths. If an image path is updated though, then it inserts a new entry to the databse for those. We don't change the image paths back during the uninstall since there's not really a way to tell if the user already had the full path before installing the CMPS.
In most cases, updating the images paths should take less time if the full path is already entered. Something in your server settings could affect that so that it takes longer though. If the paths are already updated though then it's not necessary to continue through that step.