If you place a worse GPU in that system, the stutter is going to get worse.
I play with a gtx460 and stutters a lot, specially during witch space, if I overclock the thing, the stutter lessens to almost zero if I don't jump travel or get in a planet or something like that. If I throw shadows///volumetric in, it starts to stutter.
I mean, the GPU is crap nowadays, but i've always experience LESS FPS, no sound/graphics stuttering like this.
I guess it's a game-related and GPU issue, overclocking my CPU does not seem to help, nor does help adjusting ram clocks or something. Just ocing the GPU.
Also bad connections only seems to make the game buggy, not stutter or some weird shing. Every time I travel in witch and It lags, it doesnt stutter, the animations just keep playing, just that. But when it stutters...