Looks like AS is wanting to expand their cooperation with AA. Not sure if this exactly helps anyone with their mileage accounts but still news nonetheless. http://finance.yahoo.com/news/american-airlines-alaska-airlines-expand-150000083.html
"Elite Level Mileage Plan members have access to preferred seating when traveling on American Airlines" So, I guess it will only affect Exit seats (which is the best "upgrade" I usually get).
AA and AS do not have reciprocal upgrade benefits for elites. Only AS and DL have that. So yes, only your coach seats are in danger.