Charlotte is written by Jun Maeda, who used to be writing games from Key.
He stopped writing galgames few years ago, after he finished Little Busters!
But then he came up with animation "Angel Beats!" in 2010 and "Charlotte" in 2015.
I think there are lots of people who is disappointed with the ending of these animes being rushed.
Since he used to write scripts for galgames, he still write the script for anime like he does for galgames.
From the galgame data website, we could know that a shorter galgame costs about 20 hours to complete, while longer ones may cost up to 40 hours, we take the average of 30 hours.
There is of course some extra things while playing galgame (such as selling moe, using up tissues), we will take 2/3 of the time and see it as the complete plot of a story. Now the real plot of galgame costs 20 hours to complete, and an episode of the anime is about 20 minutes without OP and ED. This means that if galgame has been made in to anime, it requires about 60 episodes to put the plot in completely. Most anime originally from galgame only choose one character from galgame, but there is still often some problems with the animation. There is a difference between the plot of galgame and the plot of anime. Galgame requires lots of daily life stories to have the intro, the normal plots and some moe and H scenes to make the game more enjoyable to the players, and shows the attractive points of different characters. While animation does not do that due to time and they had to focus on the main plot.

Here are some animes from Key.
There were quite some problems from the first season of Little Busters, but second season was way better, and the ending of EX was good end which received support from people who hated the game with bad end. Then anime was 47 episodes in total, almost as long as an year anime.
Kanon is also a good anime, but the plot is still limited with 24 episodes, the main character did too much things with other character which makes the events that should happen more spreaded out all together.
Some people was also confused after watching AIR, but this is a successful anime from galgame, since there aren't as much important plot and not much main female characters (3+0.5) in the game, and that made it possible to put it into shorter anime.
From Angel Beats, there was a famous comment of "The biggest problem of Angel Beats in that it is only 13 episodes", which was made before the last episode came out, just like Charlotte. I have played the game after and deeply realized that the anime is not enough for it.
Jun Maeda thought about lots of things and wrote lots of things, but 13 episodes is just not enough for it.
And here we have the problem in Charlotte again.

Well someone may say, why doesn't the animation company makes the anime into 24 episodes or even more. Well this isn't that easy, producing an anime is just like buying stocks, you could either earn or lose money. Having double or triple of the original length is been seen as having double of the risk while putting double of the money on bet. It will be nice if they earn money, but what if they lost money? This isn't a good way from the investment side.. Say it in a worse way, some managers only care if they are able to earn money or not.
As for the quality of the anime....
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...

But the label "Key" can still attract lots of fans to watch their anime, which makes the risk lower, NICE.

From the data of these years, anime is getting more and more popular than galgame, which makes lots of writer for the script of galgame getting in to writing plots for animes. There are still some people who are successful after producing anime. Here are some examples.
Such as plastic memories from this April, there are still some problems of having not enough episodes for it, but if you want to watch it as a romantic anime, it is still nice to do so. But there are some problems from episode one, it made the people who are watching thinking that the anime will end up having a deep ending, which makes the expectation higher, and made people disappointed at the end.
Punch Line from April is also from the writer of galgame, people were having high expectation on this anime too, but after watching it, people could only use confusing to describe the anime.
And there is Celestial Method from last year, moe.
People might that writers who wrote galgame needs to have 24 episodes to make a good story. But here are also some example of galgame writer with good anime of 12 episodes.
First is Mahou Shojou Madoka Magica, this is extremely successful with a lot of support.
While the other one is Yuki Yuna is a Hero. Takahiro (writer of the anime) wasn't happy with the current situation, therefore he first started Akame ga Kill manga with Tetsuya Tashiro, and then made "Yuki Yuna is a Hero". Even though there were different comments on the anime, but overall this anime has a great amount of Blue Ray sold out and high ratings.

Well, from all of these, what causes Charlotte ended like this isn't completely P.A. Works' problem. Instead it is a problem of different things