I saw plenty of flaws just from watching videos, and they frustrated me. I don't even own the game yet! The "cooldown" between launching airstrikes is annoying, and the fighter v fighter combat. Despite these frustrations, TTE mod really caught my attention. I can overlook (somewhat) the flaws in the core game due to the diversity that TTE mod adds.
There are some definite changes to the core game that should be made in order to make it flat out better, but that would be a discussion best left to it's forums. Though I will mention one thing here: ability to plan airstrikes so multiple aircraft types can launch at the same time, rather than dealing with that BS CD. Chances are a modder will be the one to do something like this to the game. Hope it's TTE guys who do it, cause just from Wolfpack's series, they did an amazing job.