Though the Jedi Order accomplished much good throughout the long span of galactic history in the Star Wars universe, they did have two major failings that consistently and repeatedly got them in trouble.
Their response to the Sith
Throughout the history of the Jedi Order we see numerous occasions where its members had interactions with the Sith, largely of a negative nature. As has recently been confirmed as cannon by Lucas Arts the original problem occurred in 7,003 BBY (Before the Battle of Yavin) when some Jedi began to expand their knowledge base, learning to alter the very life force around them and the other Jedi decided that such power could only lead to corruption and ordered them to stop their experiments. Now maybe it’s just me, but the potential to gain immortality and to restore a dead planet back to life is the kind of thing that sounds infinitely light-side. Despite this obvious fact, many of the Jedi decided that such vast power would corrupt its wielders. While I’ll be the first to admit that absolute power corrupts absolutely you have to admit that while the power they were wielding was great, it most certainly wasn’t absolute. It’s possible that such power could have corrupted some, but I doubt very much if it would have corrupted all. Now when we consider that if the Jedi had allowed their continued experimentation some would fall and some would not, we see the great potential opportunity that was missed here. Correcting those that did fall would be far easier because those that didn’t fall could help with that process, not to mention those same light-side alchemists as they would have become would have been able to aid the Jedi Order in ways too awesome and too numerous to describe. Instead, the Jedi arbitrarily decided that these experiments were too dangerous and ordered them stopped, not only missing a great opportunity, but causing a rift to develop between the main body of the Jedi and those few who dared to try something new. Innovation is apparently a path to the dark-side, who knew? The worst part though is this is a mistake that they keep making. They constantly regard experimentation with the Force to be dangerous, which granted it is, and a sure path to the dark-side, which is patently untrue. Obviously hind sight is 20-20, but there is surely a way to repair the rift. Imagine if Skywalker’s Jedi had tried to work with Darth Caedus to bring lasting peace to the galaxy rather than fight him. Did any of the Jedi ever sit down with him and really try to understand what he was trying to do? Many talked with him, but only to “express their concerns,” never for the purpose of understanding or support. If the Jedi could see past their fear of the unknown and deal with problems on a case by case basis rather than trying to head them off in a broad spectrum fashion, the Sith would never have existed, Anakin would never have fallen, and the Jedi would never have been purged, but in fact would be stronger and better able to guard peace and justice throughout the galaxy.
Allegiance to a Government
At what point exactly did the equally balanced dualistic Force that is neither light nor dark start caring about politics? What ancient Jedi book was it that told the Jedi to take the side of one government over the other? This tendency of the Jedi to take sides in matters of state has gotten them into a number of conflicts that they really had no business being a part of. In fact the only example I can think of where the Jedi didn’t make this mistake was during the Mandalorian Wars. The counsel basically decided it was none of their business, and it wasn’t, at least not beyond trying to help the two sides negotiate some sort of truce. Any other instances I can think of the Jedi allow themselves to be drawn into conflicts that have nothing to do with them or their mission. The most notable example of this is, of course, the Clone Wars. The Jedi fought in this conflict because the Republic asked them to. War is certainly not protecting any kind of Justice I’m familiar with and though trying to bring a swift end to a conflict may bring peace, what ever happened to negotiation? The Separatists just wanted to be independent. Why not just let them? The Republic decided that they would not tolerate planets that joined the Republic leaving it and they called on the Jedi to enforce it. The Jedi having been in league with the Republic so long, feel obligated to oblige despite the fact that the conflict is outside the scope of their declared mission. As a result, they get destroyed. Had the Jedi remained an independent entity, completely separate from the Republic or any other government, following only the will of the Force, they would not constantly suffer purges and conflicts. We All hoped that an older wiser Jedi Grand Master Luke Skywalker would have recognized that, however we know from the legacy era comics, that that’s not the case.
In order for the Jedi Order to truly fulfill its purpose, it needs to undergo a massive overhaul and separate itself both from its fears and stigmas and from any governing agency. Only then can the Jedi Order truly hear the will of the Force and bring balance to a galaxy in constant chaos. Of course that’s just the opinion of one man sitting in his N3rd C0rn3r.