It would help to give precise examples of what you think is wrong with the rankings.
I have had a look at Kõrgliiga. All teams are ranked in the top 20 safe 2.
One is ranked 22. Probably in part because they have lost to a D.IV team in round 1 of the last season's tournament. Pretty big upset. I see no problem the team loses a bit of ranking. And it's not a huge hit.
The second one is yours, ranked 24. You have just been promoted. If you do mildly well, your ranking will rise because you play better ranked team. If you get smashed by everyone, you may not get to top 20 and I think it's fair because that would show you are not a top level team yet, maybe not stronger than some D.II teams.
In the case of lower leagues, it's difficult to judge because leagues at the same level might be more or less competitive. Some girls are bigger than others... ah ah ah some D.II are bigger than others... sorry, I got the radio on :p
It's solved by using the rank of each opponent to determine the value of the win/loss, it's a dynamic system. Large/narrow wins are taken into account I think (or large/narrow losses).
It's always going to be difficult to compare teams competing in different leagues and which are never matched against each other but I think the current system does a decent job at that.
So please, find actual examples of flaws that we can discuss to better the ranking system.
There are some rankings far off sometimes. Mine, at the moment, is vastly inflated but I expect it to collapse quickly during the course of the season. It will correct itself with time.