Ugh, those are frustrating. With replay, I think you are trading some "game flow" for getting the call right. When the call still doesn't get made right (or is, at best murky), it's not a good look.
I think replay has been a net positive in sport. Really, I think it was almost written in stone that something like this was coming with the advent of TV coverage, especially as we moved into the era of dozens of camera angles, HD, etc. You can't show a blown call over and over to the millions watching at home and not give the refs a chance to correct it. I will say, it's amazing how often it turns out that the refs got it right in real time.
I watch the vast majority of my sports on DVR, so the stoppage doesn't really bother me, but I could imagine it becoming very obnoxious live.
The NBA had allowed foul calls to be challenged this year - honestly, I really like it. With basketball, you have so many cases where a foul doesn't just need to be un-called, it needs to be flipped. i.e. was called as a defensive foul in real time but, upon closer inspection, was actually an offensive foul. That can make a big difference, well worth the time to get it right, IMO.