Specifically the Heroes-same as WH, how armies are formed and recruited-same since R2, research- same retarded WH threes, regions- same since R2, buildings- same shit, even the pray mechanic is not so different than in WH (spent resources to get temp buffs) etc. Is there any major mechanic in the game that is not derivative from the Shithammer and Rome2 ? Diplomacy maybe, even that is derivative from Three Kingdoms.
The resources for one. That changes the admittedly dumb provinces into a non-arbitrary feature. Caps for myth units is another very reasonable addition. Outside of those, yeah, it's a contemporary Total War, but the awful stuff has been recontextualized and re-balanced to make at least some sense and be connected to how the game actually plays, as opposed to the random useless and undercooked mechanics of the vast majority of WH's roster.
1. Heroes - yes, they are overpowered and single entities outside of historical mode (they have bodyguards in that). They aren't as overpowered as in WH, though, but if this is what ruins the whole game for you, try historical mode.
2. I don't know what you mean by armies being formed and recruited like in R2. They are recruited much the same way as in Rome 1 and Shogun 2. Unless you mean that they have to be accompanied and recruited by a general? Yeah, that's a thing because the engine is shit. CA forced this in Rome 2 in order to sidestep a bug which could be exploited for infinite movement on the campaign map. This is not related to game design as much as how shit the engine is.
3. The research trees exist but are relevant to how the game actually plays, as opposed to WH's monstrously big but useless ones. If the mere existence of tech trees ruins it for you, I'd say it's a you problem, but it depends on what exactly you don't like about them. However, they could indeed be better, but it's a tough balancing act. Shogun 2 has the most "interesting" tech trees, but the civil side of them paled in comparison to the military one, so everyone went the same route every time.
4. The pray/gods mechanic - the difference in Troy is that they are quite important in order to do well. They are also intimately intertwined with what you do with your building slots. You need to build temples to get high favor with a specific god. They also grant you magic on the battlefield and powerful unique agents. It is done very well actually and it's definitely not a negative.
My point is that it's a contemporary Total War that is done well and makes sense. The battles are the best since Shogun 2 and Rome 1, the unit variety is surprisingly high and there are more relevant campaign mechanics than in any other contemporary TW. Could it have been better? Yes, but bitching about stuff for merely existing without taking into account how they exist and in what context is myopic at best.