BG's biggest drawback are it's AD&D game mechanics. Bad story...? Who cares. I read Gene Wolfe or Michael Moorcock when I want a good story. Story is a causal effect of RPG mechanics being what they are, not a defining characteristic of the genre. There are countless genres with good and bad storytelling and we do not call them "RPGs" regardless.
Game mechanics make or break an RPG. D&D/AD&D is notoriously poor in this regard which is why the designers of said game are always doing their damnedest to upgrade and improve the game (usually hindered by the nostalgia police and kids who would not know a good design from a bad one if their virginity was at stake.).
Having said all that, BG 1 & 2 are a couple of fantastic, fun crpgs. I started with and beat BG before doing the same for BG2 but if I had it to do over I would play through both games using Tutu. But if you are looking for "story" as a primary factor then I do not know what to suggest to you. I have very, VERY rarely seen good storytelling in RPGs if we are judging them compared to books written. Especially as far as 'fantasy' RPGs go. For superhero rpgs we have Freedom Force (& FF vs. TTR), which is only good story because the whole point of the game was to pay homage to not-so-great comic book stories of the silver age ( I mean I and many others think they are great but not in the same way that the Book of the New Sun is great. More like 'great' in the same way that 1970s Saturday morning cartoons are great). For sci-fi I know there are a few I am not able to remember right now.
Most crpgs, as far as 'story' goes, are in the same league as Fallout. Unbelievably stupid if you proposed such as a pitch for a novel but they serve the purpose of providing a framework for the game-action.