You have a good point about that taking stamina when it is nonstop, but only half of the field is playing most of the time wheras in the NBA all 10 players are engaging and running the entire time so that's why they need timeouts and commercial breaks (other than advertising money etc). You are also spot on to why this sport is not huge in the US. I completely agree. I also much prefer being able to take potty breaks and get food without missing something so I appreciate stoppage in play sometimes, but it does get to ridiculous levels in the NBA and NFL at times too.
Let's put it this way - FIFA doesn't need the sport to be big in the US to continue to be the biggest sport in the known universe. They're certainly not going to change things up for American sensibilities. It's up to us to either appreciate it for what it is or not.
Also, I think the officiating is perceived as "weak" simply because the types of calls the refs are responsible for in soccer are exceedingly difficult compared to other sports. Offsides is not only one of the most difficult calls to get correct every time, but is also a call where getting it wrong can be disproportionately damaging to the outcome of a game. Penalties in the box are the same way. There are lots of borderline calls in the NFL, NBA, etc that are hard to get right but they usually (not always) get lost in the flow of the game on the whole because there is usually more scoring, more plays to offset the damage done, etc. In a game where 1 goal is often the entire difference and chances are very hard to come by, mistakes by referees are simply more noticeable.
Baseball is still my favorite sport by a vast margin (the pace and atmosphere appeals to my sensibilities), but the game they call football everywhere else is definitely second on my list. I've been a Newcastle United fan for about 15 years now, but I've also really enjoyed the growth MLS has seen and having the Union games just 15-20 minutes away. Plus at 2 hours running time, it is less of a time investment than most US based sports (exceptions for tournament games that MUST have a winner and therefore have extra time/PKs of course).