I didn't know about this at all. Of all the new-Who, I consider Amy and Rory to be the best written by far, and I found the way they left the show to be wanting. They just had an episode where they reaffirm how they want to stay together, only to leave because of an episode with more holes in it than swiss cheese.
I actually liked Jenna with Matt Smith a lot, but the 11-Amy-Rory trio had something going for it no other companion or companion group had before or since, and I would have loved to see them stick together to the very end.
A lot of stuff is just down to production stuff. Like, the new machine-like TARDIS design (compared to the RTD era's 'natural technology, TARDISes are grown' look or Smith's 'fairytale' look) was actually first planned/intended to be shown only after Smith left for the new 'back to basics' Doctor, but then they moved studios partway through Series 7. Smith's original TARDIS interior was built on top of what was the Torchwood hub (look very closely at the shape of it and you'll see the upper/lower levels are all in more or less the same places), which was an interesting set as vast amounts of it were actually concrete. This meant that when they moved studios they couldn't just rip it up and put it back down like they did when they moved Tennant's TARDIS between series' - when they pulled down Smith's set, a lot of it was in massive disrepair and half-destroyed as a result of how it was built. It would've been just as expensive to rebuild that as to build a new one, which Moffat knew they'd planned to do in a year anyway - so they just put the new one in earlier.
To be clear, Karen & Arthur would've been happy, it sounds like, to stick around through to Smith's regeneration, but there's no way they would've signed on for another complete series after that because they'd had enough and Karen had her Hollywood offers incoming. So Moffat needed to shift them out of the way a little earlier in order to get someone new in to help as a transition character.
Basically, what happened is something like this: Smith wanted an extended bit of time off to do some stage work and pursue some Hollywood work, just like Tennant had after his three series'. They granted him this, because Moffat himself also needed less Doctor Who time in order to do Sherlock, and the result was the decision to split Series 7 across two years.
Eliminating a 2013 Series 8 from the schedule and replacing it with Series 7b meant that they had a problem, though: Smith intended to leave after the 50th, that was set in stone for ages, and there'd be no time to set up a new companion. The scuttlebutt is that they toyed with the idea of having Smith travelling alone for the 50th and for his regeneraton briefly - obviously these episodes were only at the highest conceptual phase at this point - but then the deciding factor was that Moffat didn't want to write another Eleventh Hour. So Amy and Rory were instead jettisoned after six episodes, Clara introduced in the following seven (plus Christmas and her surprise appearance in the Asylum), and then she carried on through.
The funny thing is all this bending over backwards was to avoid another difficult 'everything is new' regeneration story, but in trying to avoid that again I feel like Moffat actually swung and missed with Deep Breath as a direct result. I'm not talking about Clara here, but more the setting and the Pasternoster gang -- he became that obsessed with not repeating TEH again that he crammed the episode with people we already knew, and I honestly felt like their presence ended up crowding out the whole thing. You probably could've done the same story with just the Doctor and Clara with minimal impact, but it would've given more time for this new Doctor, like the lovely scene they have in the restaurant and stuff. I find it hard to put my finger on what it is The Christmas Invasion does that makes it inherently better when it does exactly the same thing - maybe it's the choice to hold the Doctor back for the last fifteen minutes - but I feel like in running from The Eleventh Hour he actually ran a bit too far. But that's a debate for another time.
On companions, I actually think they're all pretty much equally written. Donna remains my favourite, and Rose remains the one who I feel is best written, but I think they're all pretty excellent. Amy (not so much Rory - he was excellent from the word go) took a bit of time to grow into her potential as a character (the sort of time the likes of Donna and Martha were never afforded but still managed) but she certainly got there. In this, I do think Clara is the weak link, even if I think Jenna herself is fantastic.