I've had a MK7 GTI and now an R. The suspension/ride is absolutely definitely more compliant in the R. And my GTI was on 18's - the R is on 19's. I'm not sure if its a springs/damping issue or (more likely imo) the extra weight / weight distribution that makes the R feel like the more composed car on the bumps.
@OP if its mainly motorway driving you do, then there's really not much between a GTI PP and an R. Its on the backroads where the significant extra grip in the R comes into its own. Or even around town, coming off slippy roundabouts, etc, the grip and traction is on another level, so in those circumstances you might miss what you have in the S3.
Running costs barring fuel are much the same. I used to average 33-34-ish in the GTI but it's around 26-28 in the R. But with a lot of relaxed motorway cruising you'd approach mid 30's in the R and near 40 in a GTI.