The absolute best thing you could have done was to complain then and there -- you didn't mention if you'd done that. The second they sat you, you should have requested seating in a quieter area. Since it was lunchtime, the seaters were probably filling in the place from the back, so that as it filled up, all the seats were full. But that doesn't mean you can't request a different table when seated. You could also have requested a different table even AFTER you've been seated, if you're uncomfortable.
As for Priority Seatings ... I'm sure the reservations folks told you that they are not the same as reservations. It means that you'll be seated at the next available table. Regardless of how empty the restaurant looks, there may be many reasons why you couldn't be seated immediately.
Having said all that, if you want to complain, you'll get a lot farther with an actual letter than with an e-mail. You should address your letter to :
Guest Letters
Walt Disney World
PO Box 10000
Lake Buena Vista, FL 32830
At the bottom of the letter, write ATTN: SciFi Diner Complaint. That will get it quickly to the right people.
Be as specific as you can about dates and times, CMs that helped you (or not), and how it impacted your trip. Try to keep it all to one page. If you expect something in compenstation -- a free meal next time you visit, for example -- mention that in the letter. If you want a response, mention that too. Disney gets lots of letters each day, and unless you specifically ask for a response, you probably won't get one.
I'm sorry you had a bad experience at SciFi! Hopefully other experiences during your trip made up for it.
