I honestly don't think killing the villains off was a big deal. Especially when Doc Ock died off screen and could comeback. Spider-Man has a plethora of villains. They could have kept that going.
It isn't a big deal. 007 has been killing most of his villains for over 50 years...still going strong (stronger than ever, some would say). Also, Spider-Man has one of the richest rogues galleries in the genre, as you mentioned. The character certainly isn't starving for good villains, and plenty of franchises, especially recently, have shown that they can bounce back from creative missteps. The Fast franchise is, for me anyway, probably the best example of this. I hated every single on of those movies until the fifth one, which blew me away to the point where I was questioning whether this was indeed that same franchise.
I'll go ahead and declare that X-Men has been redeemed after First Class, and although I didn't particularly care for The Wolverine, it was a step in the right direction and nowhere near the abomination that Origins was. In all fairness, the next one, two, or even ten movies in this franchise could be stellar for all I know. If it took Vin Diesel & Co. five movies to get it right, then it could certainly happen to any other property...but the difference here is that I was always indifferent towards those movies...I wasn't
invested in them. I would only ever watch them tagging along with friends or colleagues. I'm an avid fan of Spider-Man, so in this case, my faith has been shaken to the core, and I don't have any reason to believe that things will get any better. I surely hope it does, because I'm the type of person who will forgive the mistakes of the previous entries if the forthcoming movies start to pick up steam, as DoFP
seems to be doing. Of course, that remains to be seen. May be an even bigger blunder than this movie was, but I hope not.
Captain America just can't be the only good genre flick this year. I've gotta say though, it's nice to be able to say something like that, if nothing else. Fifteen or twenty years ago I wouldn't even be wondering if Hollywood were tossing the idea of a comic book movie around. Kinda feel spoiled...but I'm rambling now, so I'm done.