So you'd counter balance with balance? Then just win with better skill or something? I'd rather win with unit composition, LOL.
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Early on, scout/LF will actually work. Scouts can kill the enemy LRF fairly quickly, which then leaves only flaks that your light frigates can clean up. With the right capital ship on the field, you can get a lot of momentum early on. This is particularly useful for Advent, but won't work as well for Vasari due to their weak LF and scout. Support cruisers, particularly the hoshiko are great choices to back up your army since LRF and flaks generally don't kill them easily.
Carriers are a great selection. Even if flaks are on the field, with the right kiting and maneuvering you can whittle down enemy LRF numbers. However, this is definitely a more micromanagement-based army so if you want to win with pure army composition this isn't the path to follow.
The best counter to LRF/flak (repulse notwithstanding) are heavies, preferably backed up by support cruisers. Unfortunately, it's entirely possible for Advent illuminators to brute force their way through enforcers with sufficient numbers, so Vasari is kinda in trouble, but in every other matchup heavies will do the job. As you mentioned, they're also high in the tech tree and probably not viable.
Unfortunately, beating LRF/flak by army composition alone is very difficult. It simply offers the best performance for your money, and between those two units almost every unit type in the game is countered. You can counter it early-game quite nicely with scout/LF but that doesn't scale very well later on and a smart enemy will bring out his own counters anyways. You can try carrier-spamming with bombers, but again a smart enemy will bring out his own counters.