Hands down go with Etihad. I just made a similar connection from JFK on the EY A380 F to QR F to DOH and it was a huge mistake! You don't have access to Etihad lounges in transit because you're not connecting to an Etihad flight. I got sent to the Al Dhabi lounge in Terminal 1 where Qatar flies from and it was not the experience I was expecting. Also the Etihad ground staff were downright rude every time I said my connection was on Qatar and not Etihad. Another issue is I booked myself a 20 hour overnight transit in AUH and they refused to interline my bags because it was overnight and not on Etihad. I was forced to get my bags in Abu Dhabi and pay 200 dirhams to store them overnight then recheck in the morning. They said had I been connecting overnight on Etihad they would store my bags for free. Another point is QR F short haul and EY J short haul are both recliner seats like US domestic first class so for the 45 minute flight there's not much difference. You don't even get access to the Qatar Al Safwa lounge in DOH. So in conclusion make your ground experience a lot nicer and just stick with Etihad.