So, you are blaming the game for you not being able to just wield your melee weapon... when there are several enemies with fucking guns in different places... at several tens of meters from you... In a FPS with some TPA mechanics to support the FPS mechanics (Itakagi confirmed this plenty of times).
...I see something absolutely wrong with your statement.
I agree with you that the game being too linear, in the online features and in the technical aspects. Aside from that, I completely disagree with you.
The game is difficult. That's it. Is not unfair, is not terribly designed... is difficult. There's only one time I really felt that I was playing something actually impossible (some place with snow and tons of heavy guys with miniguns). Aside from that, it was a challenging game, I died a lot of times, but all of them were my fault in some way.
The bosses are meant to be a one on one duel. They want you to use mainly your melee weapon. But even with this, your fire weapon still can make the difference. It does not make as much damage as it does against normal enemies, but if you use it when the boss is stunned or when your are on its back, you still can do some damage to it without getting yourself too close to him and putting yourself in danger. Of course, bosses have some distance attacks that will prevent you from overdoing this. But that's the thing: you must find the balance between hand to hand and distance combat. As for the on hit kill... if I recall right, almost all of them do not kill you instantly, but letting you with 1 hp. Also, I think they have a visual effect that allows you trying to dodge them. That's not unfair to me: just try to evade it, and if you can't. run and doge till you've recovered your health. Sure, sometimes you'll die trying to escape because of a bad doging... but that's a small mistake on our part, not on the game design.
As for the stoy, if you haven't understand that Ivan is in jail for terrorism (he was part of the terrorist gang that are now the leaders of SOD) and that he was caught because he regretted some things he did and he surrendered to authorities... then you pretty much have no right in calling the storyline weak. It's not a masterpiece, but neither a piece of shit. Is just as good as it need to make the campaing progress without being too silly.