I'm surprised that fans are unhappy with this episode, I loved it...
I thought Bryan Cranston was wonderfully poignant about how he contaminated his life (by letting Jane die)... I feel as though that's what the fly represented - contamination. He could live (and die happily) with everything up to that point. And, that was
a lot to live with - cooking meth, lying to Skylar, killing a drug dealer (in Jesse's basement), before attempting to kill Tuco...
I think Jesse's mention of his Aunt's obsession as a symptom was simply his attempt to find out if that could be the explanation for Walt's obsession with the fly... Which Walt assured him, was not the case...
Walt was a bitter disappointment to himself long before he was diagnosed with cancer and took up the drug trade... the man threw away a brilliant career with his business partner because he couldn't handle losing the love of his life? It didn't turn out like Jobs and Gates... both going their separate ways to make a name for themselves.
I feel like Walt's regrets are his real cancer... Instead of becoming Jobs or Gates of the chemical/biotech industry, he's going to make millions by producing a "poison" (as Jesse pointed out) with a man who could kill him at any moment (Gus)...
of course he's depressed, suicidal, and obsessed.