XP/SP was overhauled once, back I believe with 1.15 when they changed it to be a static amount based on kill rather than on skill use. Everything since then has been a tweak, or a change as a side-effect due to the overhaul of another major system.
Battle Regimens simply got removed, never tweaked. It is going to be re implemented as something else but was suspended temporarily as the BR system would have to undergo drastic changes alongside 1.19s large changes to stats and attribute changes. The BR system, as it was, was not worth all the effort it would require just to have it continue to function the same. A better system was needed, and a better system we will get.
Stat-point allocation is in the process of undergoing a single overhaul. With 1.19 we got the new system, and with 1.20 we will get an update to it in the form of bonus points we can allocate. A single, two-part overhaul. It can't be counted as two, considering they announced that it would be done in 2 parts before 1.19 went live.
Levequests got overhauled with 1.19. I can understand the misconception here though, considering they were the prime content of the game for so long and thus their rewards had to be adjusted each and every time a major system in the game went through an overhaul or adjustment of their own. They were never overhauled into a new system, however, until 1.19.
Overhauls are happening once. However these systems that come together to make this game are so intertwined that you cannot simply overhaul one and leave everything else as is. This is why it feels like every system is undergoing an overhaul multiple times whereas in fact it is one time for each system while other systems get adjusted to work well with it. Those are tweaks.
Their direction for the game is very clear to them. They even have the plot written out to the end, as Yoshi-P already stated. Version 2.0 has already been built, and has been worked on for months now. Considering 2.0 is what this game will become, our destination, their image must already be clear. I've had a good idea of the direction ever since they first announced the job system and with each and every update my understanding has been solidified. I feel like I know very well where the game is headed, with the bitter and the better.