The writers have said in interviews repeatedly over the years they write from from a character-mindset perspective. e.g. how would Walt react in this situation, how would Jesse react, what are they thinking and what action makes sense with the character's current headspace etc. Every aspect of the show makes sense viewed from that lens. And they've never once hinted at fan reaction ever driving or significantly influencing either BB or Saul. And BB's meteoric rise in popularity only happened when the final episodes were airing, Seasons 4 and 5A only saw moderate viewership bumps.
Obviously nobody wants anything ever to be unsatisfying, writers included, and not having a final scene between Walt and Jesse would've been given the story. Nothing about it felt "fan-servicey" or forced, it's a pretty natural and gratifying ending for both characters; while Jesse likely has a hatred of Walt (due to his inadvertent involvement in his imprisonment), he respects their relationship and bond too much to kill him. Not to mention Walt just saved his life. Simultaneously, he rejects Walt's final attempt at manipulation and gets Walt to acknowledge, for the first time, he wants this for
himself. "
I want this? No,
you want this. Nothing happens until you say that". It's the end to Jesse's character growth, him becoming fully independent.
Their confrontation fits especially considering
the similar scene with Skyler earlier in the episode. The finale is the first time Walt ever admits he did this for himself, lying and controlling everyone along the way. The scene also goes well with Season 5 in general, since it's Walt at his worse and most manipulative, particularly in his relationship with Jesse. He manipulates Jesse into breaking up with Andrea, skipping town and abandoning everything, and about Mike's death. The parallels between their final confrontation and
this scene are obvious and brilliant.