I think everything you described was pretty minor in the scheme of things. The story wasn't anything special, then again no games really have good stories. The dialogue was pretty lame, but I didn't play RE for a good story or acting. I will also give you that the puzzles weren't that great. The HUD was a minor complaint, and the merchant....that's kind of reaching. It's like me saying I don't like the game because of the title screen.
However 95% of the game, the GAMEPLAY was fantastic. Great AI IMO, and a large variety of enemies and bosses, and ways to kill them. The game also had numerous variations in the shooting such as the boss battles, helicopter near the end, and mine cart ride. The story was also intergrated to the gameplay so that you could never put the controller down.
Also maybe I am just not that good at games, but I found the game pretty difficult, especially the bosses/mini-bosses. I am glad there was adequate health and ammo, I hated running past enemies in prior RE games.