Even if it’s not the best ship, the entire point of the fight in space is to hold them off long enough for your team to finish its mission. The whole thing is essentially a suicide mission. If it fails, it won’t matter how many great ships for stealth operations you have, everyone will be dead. Taking any ship out of that battle to pull one soldier out is a terrible idea. The Normandy doesn’t have to destroy any Reapers for the mission to succeed, it just needs to keep them busy.
I agree with you on the ending options, though. Shepherd can live even without the Extended Cut DLC. When I beat Mass Effect 3, I didn’t hate the ending. I didn’t love it, but it was fine. The intense negative reaction was unwarranted.