every critics are matter of opinion of someone. but even it is just opinion, it can be fit well with game's real problem. why markers of fo3 are criticised? think about Fallout 1(or older RPGs like Wizardry).But in this instance, "flaws" are a matter of opinion. You call the FO 3 marker a flaw, other's praise it as ingenuity. This cannot be judged on a basis of facts, but is rather biased toward the individual opinion of the dedicated consumer
Fo1 for example
If you know where is Necropolise and you can get waterchip there, Shadysand and Junktown became useless. but you don't know where to aquire waterchip. so that's the reason why you have to search and asking around where to find waterchip at Shadysand, Junktown and Hub. and while you searching waterchip, you might do some favor to some people which is called today a quest. but it's not a quest, it's just small task. and whole experience of seaching waterchip(aquiring information+small tasks) is a real quest. not a stupid task to watch some horrible story.
but, what about fo3? there is nothing you have to search or think but just walk to where marker leads to. there is no quest because your primal goal, small tasks and informations(actually it's meaningless background story) are seperated each other. and it's not hard to know because journal indicates that only one task is connected to primal goal. and worst of all, you know everything what you have to do by auto journal. so it is pointless to aquire informations or helping small task for information or favor to help your journey to achieve you primal goal . so there is no quest at all at fo3 but stupid killing or walking tasks with stupid storys that are nothing to do with each other. I'm not calling fo3's storys and tasks are stupid not only because it's writing is bad but also because they don't work as a RPG's elemets. so, fo3 is just FPS with storys and tasks. but was fo3 good as FPS? or good as story teller? I don't think neither of content of fo3 didn't worked well. actually, if they tried to make fo3 a RPG, they can make fo3 closer to Morrowind which is better RPG than oblivion or fo3. but they didn't. instead of RPG, they choosed FPS+JRPG( or story telling RPG) with poor FPS mechanism and poor writing.
in short, quest marker and auto journal killed quest from quest based RPG.
so, those systems should be criticised.
but at least, they should try to make better. but they didn't. they tried to make worse as a RPG.To expect a game to be perfect, or even near perfect on account of bugs, or whatever, is expecting the impossible.