I think the concern here about substitutions isn't necessarily the performance of the teams, but the fact that it is meant to be a clan vs clan league.
Essentially you start turning every game into an "all-stars" type of game instead of clan vs clan.
To preserve that, I think maybe we should have a more strict policy on the amount of substitutions?
For example: If you fly (or crew) for your clan's official team for the tournament, you may only substitute for one additional team in your division. You may sub for up to 2 teams out of your division. If you are not an official member of your clan's team, you may sub for 1 additional team in each division (2 for your division, 3 for out of division). You may sub an unlimited number of times for your own clan's matches, but doing so counts as one of your teams.
Furthermore, perhaps each clan only has a certain "pool" of replacement points for each season. We want to play clan vs clan, not friends vs friends (I get that this is often the case, but I think at least in this league, the concept of a clan is important). You get 2 replacement points per game (cumulative over the season, so you can save up replacements), capping out at 5. Pilots cost 2 points, engie/gunner replacements cost 1 point.
This way you can almost always pad your team somewhat, but not so much that an entire ship is subbed in (unless you save your points, and only up to 1 entire ship). These numbers could be tweaked.