Yeah, there's no way Felix would get in over Isaac. Isaac was the main protagonist of the first game, a party member in the second, and one of only a couple of the original party members to show up in Dark Dawn (I know Garet did as well, was there anyone else that appeared physically?). Isaac quite simply is the protagonist of Golden Sun, there is no "oh everyone is the protagonist" thing going on like with ARMS. If Felix was more important, Matthew would've been Felix's son and not Isaac's.
Side note: I am really tired of people asking "ok Golden Sun fans, would you be ok with Felix/Matthew/GS4 protag over Isaac?" In the past month I think it's been asked like three times, and the answer, every time, is "we'd be happy it's Golden Sun, but it would be really weird for it not to be Isaac." It would be like adding Luigi before Mario: yes, they're both super important, but one is clearly the face/main protagonist and it would be strange for him not to be the first addition.