We are at v13 and there are still 3 more versions to go. I think rejuv has mostly kept people glued to the game is because of its mysteries.
1) Team Xen
Personally I believe that its good that we still dont know what team xen wants. All we know is that they wanna wreck havoc on the land but not just for the sake of it. Madame X knows something that the chars and we dont and it plays to the part of the mystery. Rest of the team xen is fodder when you take this into the picture. They are doing X's bidding and nothing more, nothing less. With 3 more versions to go, I think the best time would be to reveal this mystery would be v15, v 16 being the conclusion of it all.
2) the interceptor
Now here I think where the devs have actually made everything boinkers. Until v12, interceptor was someone who was outside all that fate circle and whatnot. Now we do get answers in v13 as to who they are, but I wouldn't really call them answers. With what was told came other questions. During the obelisk arc, we were told that the interceptor has adrest's soul and is being co hosted by crescent. That the world has already been resetted once if the interceptor is here. This made sense as to why the third badge existed but was not recognized by alex. They went back in time to the prev world and got the badge from there. But then we do not get how long this reset happened. Then later on, the interceptor is now someone made by a black magic box and has multiple souls and is yet controlled by someone entirely else(the person we name at the start of the game). Oh and he has archetype too. If the world was resetted why do we see al these garufan tech and ruins everywhere? in what sense was the world then resetted? And adding to that, they used tech of the parallel universe to put the soul of our guy into the body of the protag.
3) Too many characters
I totally agree that there are just way too many characters to even keep track off. I get that you can have countless side chars but everyone here is trying to be the mc. As the guy above said, making the story too much convoluted. It can be argued that with this many characters, it brings a variety and makes for a richer storyline but here i feel that a single type is being repeated by many different characters.
4) Sudden introduction of unreal mechanisms.
The ligosomnia engine and the parallel universes. Not the time travel part though. I think it was given adequate time and executed nicely even though there are some plotholes left here or there as said by the above guy. But the big problems are the 2 I mentioned. We got introduced to the ligosomnia engine and then it gets destroyed in the same chapter. For something that has such a major role into our story it doesnt get much time nor does it get a good execution. And I fell that the parallel universe was more of a name throw to give an origin story to clear and kearan, and wont be more than anything. I maybe wrong here because obviously anything can happen in later version. Though now what i do want to know is who and where are tiempa and spacea. They could have been human manifestations of dialga and palkia but then you see how giratina is being treated in this game and it feels far off from that.
The Story is good but is really very loose. We dont want a masterpiece as some guy above said but i guess a clear and crisp storyline has to be there even if there are 3 more versions to go. I remember the devs saying in some qna that the storyline has already been set and its not gonna be changed but i think that the devs do need to think about how the execution of it all is going to take place.