I agree with OP that the games were a foggy mess, but other than that, completely disagree.
I have over 50 great games on the little machine. Sure, most of them have aged terribly, but so did everything on Saturn and PSX. It's not something N64 related. And yes, there was a lot of fog in most 3th party N64 games, but I take that fog over the warping pixels of your average PSX game any day of the week. I sold my PSX and bought an N64 around 1998 and never regretted that decision.
I absolutely loved the controller. Sure, they broke easily and felt as flimsy as any PlayStation controller, but they were the most comfortable controllers I've used so far - beating out the X360 and NGC controller. It would be perfect if they were build to last, but ow well, can't have it all.
About the games - I guess the N64 didn't have a whole lot of games, but I still managed to collect about 50 awesome games in it's lifespan. That's more than one game per month - on a single console. I know some people on Neogaf play like 5 games a month, but for me that number is crazy good. There's only 2 devices I have more games for - one of them being the Game Boy, which was 'current' for a good 10 years, and the other being the X360, which again was 'current' for 10 years and had loads of games that can be bought for peanuts.
Also, most games on N64 I consider to be among the best of that era, with near infinite replayability at the time, so that helped as well. Games like Super Mario 64, GoldenEye 007, Pokémon Stadium 1 & 2, Mario Kart 64, Super Smash Bros, Wave Race 64, 1080 Snowboarding each saw 100s of hours of playtime, either in single or multiplayer. And Paper Mario is the only RPG I ever replayed besides the original Pokémon games (3 times even). And then I haven't even begun about the multiplayer possibilities of the little thing.
Anyways, to answer the OP's question: No, to me it's one of the best era's Nintendo's had. A lot of my best gaming related memories are on N64 and no one's ever gonna change that. The worst Nintendo era is easily the Wii for me. That era did everything wrong and produced maybe 6 or 7 good Nintendo games in a timespan of 6 years. Thats abysmal.