Well, it's an opinion question because they are both very good motorcycles......BUT....There are performance categories that have shown on to be better than the other in different areas....
Looks....I'd say the R1 is the best looking
Motor.....Both being stock I'd give it to the Suzuki for all out performance. but they are both so fast it shouldn't matter too much to the average guy...
Handling.....Some people like different flavors of handling...Personally, I like something solid and stable so I'd say the Suzuki...I've ridden an 02' R1 which is esentially the same as the 03' and it had a stinkbug feel to it and was a little twitchy.....A steering damper and ride height adjustments can fix this....
Comfort...I'd say GSXR.....Both have gel type seats but the GSXR is thicker and for me it feels the most comfortable....However, this is just another opinion as some will think the R1 is more comfortable...
Quality....R1