I like Steins;Gate a lot, but (and I've found this with Chaos;Head too), I think it's not that obvious how the choices you're making are actually affecting the route you're taking through the game. My experience with VN games isn't that extensive, but generally with the other ones I've played, it felt easier to understand what the choice you're making was going to affect - Steins;Gate can be a bit obscure in that regard.
Even without comparing it to the anime, I also thought the early part of the game was quite long winded. Not as much as Fate right enough, but it takes a good number of hours before the story really starts in earnest, and there's a fair amount of infodumpy lecturing from Kurisu to get through too.
