The Fabulous Five:

Reworking my rankings again, I came to this conclusion:

1. One Piece (1999-2014+) (550)
2. Fairy Tail/Rave Master (2001-2014+) (159)
3. Naruto (2002-2014+) (336)
4. Dragon Ball (1986-2014+) (381)
5. Pretty Cure (2004-2014+) (520) 
 
Why did I put these five up top?  The answer is simple, these are the longest good series in anime that at least still have a chance of reaching their endings.  If one of them doesn't reach its ending, then of course it would be kicked out of the group, but until then these shows are the most promising.  Not only are all five of these shows already among the longest shows in anime, but they're all still getting longer.  It's hard to compete with such titans of both length and progress.  Bleach might have been up here with the others, but it didn't receive an ending like these other shows will.  In addition, it has a lot of straight out bad material when it's trying to be funny instead of serious, which is just a waste of everyone's time.  Humor is great when you can pull it off, but the author of Bleach just isn't in that league.  If the joke/dumb sections of Bleach were edited out, it would have been a much better story, but unfortunately those portions are genuine canon and so all you can do is shrug your shoulders in frustration.  Hunter x Hunter is just a fundamentally flawed series.  Not only does it lack an ending, like Bleach, but the end of the chimera arc is one of the dumbest trolls an author has ever written.  After the story spends its whole time building up how powerful and dangerous the King is, it turns out anybody with a nuke can easily take him out, and that any pipsqueak nation can afford to kill the King with one good jet/artillery piece/missile/suitcase bomber/whatever.  In that case, what are all these Hunters fighting with their lives on the line for?  Why are nen powers even developed in the first place if modern military hardware is still superior?  It just makes a joke of the whole series, of Hunter's very reason for being, when they would have done better to train as soldiers in the military, because everything they can do technology can already do better so there was no point to any of their training at all.  Inuyasha is too episodic and doesn't flow as well as these storylines.  Sailor Moon might be competitive, if its whole series were remade like Dragon Ball Kai has been, but that doesn't look like it's going to happen.

The point is, length alone can't get you to the top, but it can get you further than anyone else so long as it doesn't trip up along the way.

What the top four shows share that no one else has is:

A high degree of quality.
An enormous length.
A continuous story where each episode ties into the next.
An ending that will actually get animated.

Until you have all four of these features, I just don't see how you can compete with a series that has all four.  All four of them are multipliers.  For instance, a lot of good episodes is X quality times Y quantity.  An ending at least doubles the worth of any series.  And the fact that all the episodes in a series are connected to each other and reinforce each other makes them around 10 times as good than if they were just stand alone random eps.  Inuyasha's average quality is lower than these four series, and most of its episodes are pretty much pointless and have no relation to any other episode in the series.  A typical Inuyasha arc runs something like this:  Naraku creates a villain sidekick.  Inuyasha defeats said villain sidekick.  Naraku creates a new one.  Repeat.  Or just as bad -- Naraku gets a powerup.  Inuyasha responds by getting a powerup of his own.  Repeat.  Situations like this just end up with the series treading water, going nowhere.  Inuyasha had more of that than any other shonen action show, which is why it ends up falling so far behind the others.

This brings us to the curious case of Pretty Cure.  Pretty Cure is arguably the longest good series in anime (if you add up the length of the Precure movies the total Precure airtime exceeds One Piece's airtime of canon material.)  However, because it resets every 48 or 96 episodes, it loses the benefit of the episodes being interconnected.  Except in the case of the DX movies, which do connect all the seasons, and also tend to be some of the best Precure material out there.  But even within a season, many episodes of Precure lack any connection or cohesion to the rest of the whole.  They could be there or not be there and no one would even notice the difference.  Almost just as bad is an episode that advances the plot for around 2 minutes out of a 30 minute show while messing around the rest of the time.  Even if it technically is important to the series, I feel like the makers of the story could have written it in a different way and gotten us to our destination a little faster.

Add to this the dramatic differences in quality between one season in Precure and another, which are all completely different from each other, and that 520 number doesn't mean much.  One Piece, Fairy Tail, Naruto and Dragon Ball of course have their ups and downs, but the series all stay pretty much within a narrow range of quality, as expected of a show where the whole plot is one, all the characters stay the same, and the writer of the whole story is the same.  Quality can only vary so much in a case like this.  Precure isn't like that, so watching Precure is a little like eating assorted candies of varied worth at the end of Halloween.

For this reason, Precure exists in the weird twilight between long-running epic franchises and short-running individual series.  Putting it as number five reflects this reasoning, instead of the natural '#2' or even "#1' you'd expect from its length.  It doesn't have as strong multipliers as the top four series have, even though it does have all four to some degree.

6. Clannad (2007-2009) (48) 
7. Sword Art Online (2012-2014+) (26)
8. Little Busters (2012-2014+) (44)
9. Higurashi/Umineko no Naku Koro Ni (2006-2013) (86)
10. Bake-(etc)-monogatari (2009-2014+) (54)

Which brings us to 6-10.  These are the series that haven't primarily relied on length.  SAO and Monogatari sell well so they'll probably receive an ending someday.  If they don't, like if Fairy Tail or One Piece don't, I'll have to revise their rankings then.  The series are decently long, but nowhere in the same league as the top 5.  Umineko makes up a huge portion of Higurashi's length, but it's worse and lacks an ending of its own, thus dragging that show down.  Clannad and Little Busters have an ending in one sense, but in another they don't.  Clannad lacks Tomoyo After Story and Little Busters lacks Kud Wafter.  So you can only give those series a .5 multiplier for that.  Their quality is as high as can be asked for, but their continuity is a little suspect.  Visual Novels, after all, are choose your own adventure stories where you go off on entirely different routes that have little to do with each other.  The anime tries to string all the parts together, put it still feels like a loosely woven basket that water would fall through in an instant.  At best you can say that parts of the show are tightly interconnected, unlike more standard manga-based series that always stay on track from beginning to end.  So as you can see, none of the 6-10 group can claim to possess the 'big 4' traits that the 1-5 group has.  These shows are generally better than the top five in certain limited ways, like strength of story or uniqueness or memorability of characters or artistic beauty, but none of that matters in comparison to length, an ending, and continuity.  It's like all these shows are being divided by their weaknesses while the top five are being multiplied by their strengths.  In such an unfair competition, being 'the highest quality, ep for ep,' just doesn't count for much.

In the end, the Soviet Union outnumbered and overpowered the Third Reich, no matter how much better they were on the battlefield.  The story of good anime ends up looking much the same.  You just can't beat quantity.  There's nothing like quantity.  Quantity has a quality all its own.