Regarding Into Darkness, while it did make more money overall than Star Trek '09, it didn't in America, and I think that's very important because that's the sign that Into Darkness had lost the biggest Trek audience. While it did an admirable job appealing overseas it was not as well received domestically, and Beyond suffered because of that. It's like with other movies where the first one is very successful and the second one gets the benefit of that, but if the sequel is lackluster, the third film doesn't do as well.
When it comes to Into Darkness and Beyond I agree with those who felt it was too long between Trek '09 and Into Darkness and that the revival of Khan was a mistake that eventually bit them when it came to the lack of interest in Beyond. I also agree with those who found the Beyond marketing not good. Paramount/CBS did little to take advantage of Beyond coming out in the 50th anniversary year of Star Trek, and it also didn't help to go after fan films around that same time either.
I wish we had gotten another film say around '11 when the brand was still hot. Even though the Star Trek Kelvin video game with the Gorn was derided, I wish they had adapted that story for a film. It would've played more into exploring new things with Trek, as opposed to retreading Wrath of Khan, the Holy Grail of Trek films that was bound to end in disappointment.
As for my feelings on Into Darkness I really disliked what they did at first, but I can now appreciate the moviemaking aspects. It was a well-made, well-acted, and fast paced movie. Benedict Cumberbatch made for a great villain, but he was no Khan.