Not a Fischer expert, but I'd say he was his own weakness.
What Were Bobby Fischer's Weaknesses?

a) I've heard he didn't do well with "irrational" positions. He was of course very good in sharp or complicated positions so... I guess irrational means no standard pawn structure and many pieces on odd squares where both sides have yet to organize around an idea (perhaps because many tactics left them on odd squares).
b) I don't know. Likely some openings that were fashionable at the time / analysis he did that has continued to develop. So obviously he'd have to catch up on opening theory.
c) He'd be an excellent player today. He wouldn't have to modify anything IMO (besides learning anything new in the openings of course).
You can learn from his clear and technical play. Things like playing against a static weakness and transitions. As you said he was very good in endgames, which IMO falls under technical play.

IMO fischers greatest weakness was his materialistic nature take a look at this game where he gets crushed by tal for being greedy with material another one of his weaknesses was his inflexible reportatire he used the same openings and he developed a sort of predictability other than that he was a great player
Fischer struggled on the white side of the French Winawer.
He lost his way in complications. Also, he drifted in situations where no clear plan was available. He worked hard on these defects and became world champion.

I think the biggest weakness to his career was himself. He could have had a long and prosperous chess career. While there is still talk of him being the best of all time, he simply didn't prove it.
It's a shame. If he continued to play and defended his title (as a champion should) he may have dominated chess right through to the early 90's rematch with Spassky and beyond. He was obviously still very strong after a 20 year absence from the spotlight.
The thing is, I don't think he could have done that. Hey, we'll never know.
As for his actual game, he seemed to be very strong in endgame scenarios.
Also, something which seems to be overlooked, he had great endurance. That really can make all the difference in a long complicated match. It has been seen a few times in long world title matches. Some people begin to fade with each day. They become tired and mentally drained, leading to their game suffering. To me, that is an ability that really makes all the difference at the top level. Especially when you have many players of near equal playing strength.
I am not strong enough to even pretend I could accurately analyse his actual playing ability. This is just an opinion based on things I have read and games I have watched.
What I find so sad about Bobby Fischer is that if you go to youtube and watch his lectures in the 60's or the interview that Johnny Carson did with Fischer in the 60's, Fischer is quite a likeable guy, even confident and charismatic. You would not hesitate if you met him then to show him your game and get some chess advice.
But then what a contrast with Fischer post mid 1970's. He became bitter, his communication skills and likeability vanished, and he sounded so crazy that you wouldn't ask for his autograph.
That is the saddest thing for me. What happened? Maybe you would have to have been around him before and after both periods to answer that.

What were Fischer's weaknesses? NONE OTB, for all practical purposes; although some of his peers claimed he was slightly weaker in the middle-game than in the openings and endings. Some GMs claim his stubbornness in certain openings ie in always playing 7.a4 vs the FD Winawer Var. made it easy (or easier) for his opponents to prepare for him and get better results than if he had been more open minded, but then how do they explain his successful "stubbornness" in playing the Najdorf SD PP Variation and SD Fischer (nee Sozin) Variations so often?
b.) What parts of his play/game have been proven wrong over time? There are various examples in his 1972 WCH games, click on the link below:
http://www.chess.com/blog/NimzoRoy/fischer---spassky-1972-wch-summary
Fischer is one of my favorite players and I've enjoyed watching his old games.
I have a few questions:
a.) What were Fischer's weaknesses?
b.) What parts of his play/game have been proven wrong over time?
c.) How would Fischer's game translate into today's game/play? What aspects of his game would he have to modify? (This is kind of a b2, since it's related to b.)
On the other hand, what areas of Fischer's game can we learn the most from?
So far, for me, I've enjoyed Fischer's end game quite a bit. I don't always understand the things he's doing in openings or middle-game, but with less pieces on the board, I have a better idea of what he's doing (and also from watching analysis of it online/Youtube), so I've picked up some things from that.