don't forget that managers, coaches and players have also learned how to play us - that's a major factor too
closing down players, not leaving space, knowing the runs, understanding a player's behaviour, their weaknesses - as well as exploiting them also
Opposition teams will always become familiar with teams and systems the more they play them, but it doesn't necessarily mean they can deal with it.
Let's not forget the 7-0 demolition away at Palace was on the 19th December, where we looked like everything was perfect and they just couldn't cope with us. That result meant we were top on Christmas day, and by that point teams clearly hadn't sussed us out - over a third of the way through the season and having played against this system since around 2018/19.
I think its best to reserve judgment until we've had another 'normal' season, as there are too many variables in the last 7 months to make any reasonable assessment on players, systems, or whether the opposition have 'caught up'. Although Virgil and Thiago were injured on 17th October we managed ok for a while, and it wasn't until the accumulation of injuries became too much for the system and players to bear that we really started to struggle:
Up until xmas day: P14 W9 D4 L1
That one defeat was the 7-2 at Villa - an utterly mental game where we conceded 4 deflected goals and almost every player had a collective shocker (including Virgil). We re-grouped and were top by Christmas and looking like we might cope ok in the 2nd half of the season.
After xmas day: P17 W6 D3 L8
This is the period where we started to see the real affect on the system of losing Virgil, Gomez, Matip (the first injury), plus various other players missing some games such as Henderson, Fabinho, Alisson and Trent. We also had Fabinho or Henderson playing as CB's for most of these games. The weaknesses you mention that were being exploited weren't due to the system itself - they were due to us missing 4 or 5 of the first 11 in many of the games, whilst playing different combinations in defence and midfield from late December to early April. Any team in a similar predicament would be weakened (and exploited), and City's collapse after losing Laporte last season shows the difference just a single player can make - even in a team spending billions.
It's no surprise we've looked better once Fabinho is back to his best position, and we have a settled combination of centre backs for more than a couple of games. There have also been plenty of occasions this season where we've seen mini patches of form where we could see the Liverpool of last season, but where we haven't had the luck, or were robbed by VAR, or had 100 shots but none would go in. We've also only lost 3 out of 15 away games which is pretty good for a car crash season, and doesn't suggest teams have worked us out if they can't beat us on their own turf. I don't think we've been as bad as our results suggest.
So, in answer to anyone who thinks Klopp's system has been 'worked out' - let's wait and see next season before making any final judgments. On the evidence of this season, either all the opposition teams went home for xmas and somehow magically worked out to play us, or there are other factors that affected our form and results. I know which one I'm going with.