I thought from the patch notes that only gunner flares take longer to reload now? I haven't noticed much difference as a pilot. The big problem is the change to rockets, which I've personally largely adapted to but makes things massively riskier
Guided Shell has always been bullshit. It's the most powerful AA weapon in the game, is completely fire and forget, kills helicopters instantly, has no warning to distinguish it from normal missiles that can be avoided with flares (unlike say, real life) and the only countermeasure is the weak sauce ECM which means you will basically die to everything else if you equip it. Not that many people have it yet, but whenever I see people who do they are always sitting in out of the way places in midmap not moving and racking up air kills like there is no tomorrow as they know no one can touch them. It's the vehicle equivalent of IRNV.
The counter is of course to use the TV missile, but just as few people have that, and they will nearly always be found flying the helicopter on a public server out of necessity. Even then it's now even harder to hit targets with it, and you still have the same bullshit with it doing inconsistent damage, and if a three man tank team can't repair their vehicle back to 100% before anything else gets even vaguely in threatening range, they should probably play another game.
All the helicopter nerfs affect high end play. I don't mind this so much personally, but it's going to decimate the almost entirely low end play found on public servers. there are going to be even less people actually able/willing to fly helicopters now as the skill requirements have gone up, and earning points for unlocks that make them survivable (e.g under radar) is going to be insanely hard if you aren't gunner with a good pilot for a long time.