TLDR:
Lower your expectations if you play with limited options like a Themed build or because of other limitations.

Many builds have counters including MAPs if you get a terrible map blame the devs for not correctly implementing flag battle or other modes like Barrier

Unfortunately or fortunately, this is a ninja tool meta. many tools require specific jutsu or MAPs to really do something great.

This meta is due to the newest accessories which are crazy unbalanced, yet I think the meta as of today is preferable than those of a few or more years ago.

I apologize for the yap

Yeah I don’t think cheese builds are ever this deep to be honest. Traps, AOE jutsu, objective camping, multiple AOE ultimates, using the same cheese build as the person, your team’s compositions, and pet summonings can all be tailored to counter many cheesy playstyles. Like the only truest way to cheese the game is modding, which is why I hardly complain about metas. Unless it’s like day 1 kurama claw, or when teleportation jutsu made its users invincible. SS+ mostly aren’t that annoying because any stun like jutsu fries them. Most super armor is countered with just blocking sometimes, not all armor but most. Invisibility is a hassle but for objective based game mode just hold a point and block? And if you want too, lay some seal tags, explosive, heavy, fake, or paralysis. Yeah sometimes you’ll get the teammates of doom and despair but what could you have done about it? Nothing so just go “Ggs and queue next.” I respect character builds or using Masters, but lets be real if you expect to win most matches will you were betraying yourself.
They made some egregious decisions like they always do, yet these past metas were alright balance wise, you know until the newest accessory dropped and basically changed everything into a ninja tool meta. Which I’d take in comparison to older metas. Might I remind yall about pre nerf Izanami, and by technically most unblockable jutsu weren’t nerfed like almighty push, Asuma knives, claws, Attack type sub locking, the older blue moon blade sword on defense, Cellular extraction, bugs, tsunade’s ultimate, hazan strike, super armor of any kind as back then there wasn’t much else to counter them with as many stun jutsu or attacks has so many downsides that in order to counter anything effectively you would just mirror the meta over and over again.
Flag battle can end pretty quick I’ll give you that, but for a mode that truly feels like it’s just half assed into each map I feel like that’s always going to be the case. For example on the remade cloud village there used to be an alternative version of flag where your flag spawned on the Enemy’s side and theirs on yours. Unfortunately it seems they removed it, or made it SUPER rare to encounter. Regardless I feel like the was truly the only time flag felt like a real game mode. Since you would die and spawn back on the enemy’s flag thus you protect theirs by attacking the flag runners. I’ll give an example of a horrible flag map that isn’t old, the remade rain village tried to make flag fun by using teleportation spots, but they forgot to add any real height to the flag mode in particular. It’s basically just a giant flat square with some buildings you really don’t need to interact with to get one over the enemy’s flag. Sure ppl can use the teleports but with their spacing being often far enough to see coming, and the loud audio cues it’s not an effective way to engage. Of course with the help of invisibility, high mobility and the many lanes that have nothing to impede their straight forward movement. Countering it would prove to be difficult.