Firstly, let me say that I am not well (I mean in real life), but I will try to give an answer. I came to post about what many have been complaining in the recent weeks after the latest abnormal one I observed from my game account. I cannot say things at 100% confidence as I have not thoroughly made experiments throughout all those periods, but I can say some things say to a good percentage of confidence.
There is something that you call a 'troll' or an unexpected result that occurs once or twice in season, where your team would lose (or draw) when clearly it should have not. You gave a possible explanation for this as a bad roll of dice, where the game engine neglects everything else, including the formation, the orders and maybe the quality. Is that a possible reason why those occasional, unexpected or abnormal results happened? Based on my observations from all those periods, yes it is a possible reason. But, there seems to be something else, as if the RNG is biased for particular teams in certain periods because there are noticeably more abnormal, unexpected or unsatisfying results during those periods.
June-August 2015
In this period, there was only the blue versions (comment-type highlights only) of the game. The first season was like very satisfying - winning lots of games with satisfying scores, things seem to work and so on. Then the following season, another face of the game started to show up. I did have abnormal results and more than 2-3. What I mean by abnormal is not just a match lost where it should have not, but abnormal things like my team should have won by a much larger score but instead won with unexpected scores. If you remember, at some point I suspected that certain things in the game (like constructions) were having an effect as I observed those bad periods occurring only when some sort of construction was on-going and was at some progress point. In the third season, there were also many unsatisfying things, which finally caused me to quit the game. As an answer now, I would say that some unsatisfying results happened probably due to wrong tactics (formation and orders), and some may have happened due to bad number from RNG and some maybe to a combination of those 2.
March-August 2016 (New Browser Version)
In this period, the first season I got like as if a new team (tokens, packs but witha 6-star player bearing the last name of the manager). Again, the first season was like very satisfying. The scores were more or less satisfying. There was the 1-2 lets say bad days or bad number from RNG.
The following season, there were more unsatisfying results. Then later, Nordeus made more changes in the game, whereby clicking the bonuses resulted in instant effects like one more goals scored or one or more goals conceded based on what was programmed in the game was being the right or wrong bonus to be clicked. Following the assistant manager was also very helpful at that time as correct actions based his advice resulted into instant positive effects.
Then much later, Nordeus removed or disabled some things, which resulted in nothing much that happened when following the A.M advices or clicking the bonuses. The game became numb. Some things became more evident in association matches. Matches appeared to be on 'playback' whereby the results were already decided before the match was shown to be played. Later, I also did tests using several accounts, making them play friendlies against each other, and I found out that matches were indeed more like pre-determined before the match was being played and doing changes in the game (including following the assistant manager's advice) resulted in no effect on the pitch.
During the two periods, 11/12/2016 - 11/01/2017 and May 2017, what I noticed is that the game seems to be giving preference to a certain team to win a particular competition. I also noticed that a team could say have won a double or a treble in one season, and the very next season this team is like different to that team that was the previous season, and in some cases almost like unrecognisable in some way to say - things don't seem to work for this team and there are noticeably more bad or unsatisfying results; it is as if the game does not want this team to succeed in that particular season.
What is sort of new (but not really new), more like more pronounced, is the way the abandoned teams play and how they score goals against active teams. There is also that relatively high shot efficiency thing. A highlight just appears that shows a player where he shoots and it is a goal. Another example is where the player just run towards goal without any hindrance (that is, the defenders did not make any effort to stop him, as if they sold the match), go past the goalkeeper and slide the ball in the net. I even saw a situation where one player was surrounded by 3-4 defenders but still got through as if the defenders did not make any effort to get the ball of him. Of course if the player was someone like Messi, you can say he dribbled past those defenders, but not in the case of a 3-4 star attacker versus 5-6 star defenders. So, what seems new now is that a strong active team have more chance of losing or getting a draw against an a weaker, abandoned team; also there will be more unsatisfying results, that is, even if the strong active team wins, but the win will not be satisfactory.
Briefly, yes, there are differences in the game between all those periods.