Yes there were some missteps at some points (some earlier episodes had some questionable animation quality, the BGM was fairly invariable to start, and most egregiously they should never have glossed over and rushed through the previously covered manga material), but the back half has been just about perfect, with the better pacing, more variable BGM, and almost universally higher quality animation. It doesn't hurt that the story itself has built up masterfully, but I'm hardly giving BONES credit for that. At this time, it's arguably the best anime series running, and certainly tops in its genre.

Similarly, while I agree overall with the Soul Eater disappointment, I think it is misplaced. To me the only real flaw in the production was the poor writing of the anime-original elements. The parts up to the split in storyline (during the Brew Tempest Arc) were, as someone suggested, nearly "panel for panel" with a few additions to set up the later differences, but in this case it was a good thing, as the manga storyline up to that point was quite good, and—dare I say it—original on more levels than most shounen fare. Arguably the manga has since fallen into the rarely successful angst + edgy + mindscrew = good(?) formula as a large part of the dark/ironic humor that made the series so fun has disappeared, and what humor remains isn't, particularly, but the anime original parts commited the even more heinous crime of, as one person put it, being "boring". But up to that point, it had an odd design to it that no doubt turned some people off in this age of cookie-cutter moe-moe series, but no one could legitimately fault the at-times jaw-dropping and usually above-average animation, in addition to the memorable characters and previously mentioned good storyline and quirky humor.

And I also take issue with the complaints of BONES making sequels. Sequels are not inherently wrong, and certainly have their place, and that place is to tell more of the story when there is more story that needs to be told. Frankly I wish there were more sequels, and I'll tell you why. Too many times we have an arguably wothy long-form series (like FMA or even Bleach or Naruto) that gets a great adaptation up to a point, and that point is where the anime catches up to the source. At that point one of three options is taken: (#1) continue on with a divergent ending (FMA 1S, Soul Eater); (#2) make filler until the source gets far enough ahead, then adapt, rinse, and repeat (Bleach, Naruto); or (#3) stop completely and pick up later on with a new series once there's enough source to do it (Haruhi).

Not enough series do the latter, arguably due to an aversion to sequels, and both of the former are rarely literarily successful in anything but episodic series (One Piece is the only exception I can think of, off the top of my head). Having the willingness to do #3 also has additional benefits. If the later portions of the source are worthy, you can adapt again at your leisure, without the issue of having to rehash over the parts that were previously covered (#1) or sit through usually inferior filler (#2).

Conversely, there is impetus for the mangaka or original author to keep up his worthy level of work. If the hypothetical "first series" of Bleach had been ended at the SS Arc, would what's been written since, especially recently, have been worth making a "Bleach: Arrancar" sequel? Since Kubo has the studio by the short and curlies waiting for his next batch of "canon", he can write whatever Deux ex Machina drivel he wants, and they lap it up like Dom Perrignon. And since Okubo doesn't have to think how he'd follow up a post-Brew Arc Soul Eater anime series, since they already went another way at and after that point, he's already gotten his payday, and he has little chance for an additional adaptation unless he starts putting out FMA levels of quality (which he hasn't got the skill for), he no longer has any reason to try to keep up a adaptation-worthy level of writing, and so is doing an admiral job of stinking up the joint.

The problem I have with the series is the absolute butchery they did with the first dozen or so episodes of the series going all the way through essentially until the end of the first Greed arc. They had occasional break out moments like the different take on Ed and Al's human transmutation. That's essentially 1/5 of the show that they completely flushed down the drain. Don't tell me that they had to do it to get to the manga original stuff because as it stands nobody wants to watch a subpar version of the original series. Case in point: Lior and Cornello. Even recent episodes despite the overall amazing animation have somewhat toned down the violence from the manga(like not showing Envy's bones while he was being torched). However again it's really the early episodes that are a mess. Recent ones have been overall pretty great.

The anime original writing for SE was absolutely atrocious by pretty much any standards(although I personally loved the Excalibur episodes for the PURE rage it developed in pretty much everybody. Oh god those posts were funny). That's a problem I've started to notice with Bones is that their writing starts to fall apart near the end(see the original FMA, DtB2, Xam'd, and SE) as they have to do some original writing. Soul Eater was mostly about style and Bones delievered in full force there.

I have no complaints with sequels as long as they aren't crap or just go a completely and unrelated tangent in regards to the storyline which DtB2 did both.

Currently SE(manga side) seems to be focusing on back history so I would hold off judgement on that until we have a better understanding of all the characters(particularly Noah). It certainly isn't as bad as you make it out(points to Justin twist).