They set up Lyle really early on. Neil is visiting a grave, and IIRC he sees someone else has already placed flowers there. Then we see someone who looks exactly like Neil watching nearby.
I felt they did a good job differentiating Lyle from Neil. Neil was consumed by revenge which contributed to his desth, and he never really fully opened up to romance, plus he was Setsuna's best friend. Lyle on the other hand was able to control his desire for revenge, did enter a romantic relationship with Anew (even if it ended badly), and he nearly murders Setsuna for killing Anew, and even if he ultimately forgave him, their level of friendship never reached the level that Neil and Setsuna had. Also, Feldt and (likely) Tieria had feelings for Neil, whereas they do not have them for Lyle even if IIRC Feldt was briefly conflicted on this but Lyle made it clear to her that he is not Neil.
I understand if you're just not a fan of the "Backup Twin" trope, but I do feel this was one of the best executed versions of said trope.
Also a million times better than Seed Destiny just flat out resurrecting Mu La Flaga as he was DEFINITELY DEAD at the end of Seed, so they had to make the recap movies retcon his destroyed helmet being shown or something like that.