Best practice for loading webpage with long server side script
Best Practice would be for the the script to not take 10-15 seconds. 
What is your script doing? Is it generating something that you can pre-compute and cache or save in Google Cloud Storage?
If you're daisy-chaining datastore queries together, is there something you can do to make them happen async in tandem?
If it really has to take 10-15 seconds, then I'd say option 2 is must:

User clicks a link > html page is immediately returned (with progress bar) > AJAX post request to the server side > complete script > return result to html.
What is the current best practice and method of loading a webpage (that has 10 - 15 seconds worth of server side script). 

User clicks a link > server side runs > html page is returned (blank
page for 10 - 15 seconds).
User clicks a link > html page is immediately returned (with progress
bar) > AJAX post request to the server side > complete script > return result to
html.
Other options (threading?)

I am running Google App Engine (Python) Standard Environment.