This is a tough one. When you compare them, the 40k marines are taken in and trained from their early teens, with probably a far more advanced training regime over a longer period, but 30k marines were already battle hardened veterans of the Unification Wars before they underwent the transformation, with only the very toughest of them surviving, so all it did was refine them in to even more efficient killing machines.
I think the point about the 30k's being more independent and free thinking is a good one. The codex is extremely restricting, actively discouraging thinking outside the box (Uriel Ventris anyone?), so I think they may have been quicker to respond to a tactical situation, or find it easier to adapt.
There might also be an issue with the fact that in 30k the geneseed was still fresh and shiney, and may have been diluted, or worn down somewhat in the following 10 millennia. In BL fiction there seems to be a theme of the HH traitor marines thinking of 40k marines as smaller, paler imitations of the originals. While ingrained arrogance and exposure to the warp and it's corrupting, enhancing influence probably plays a part in this, maybe there is a grain of truth in it. We know there is something to this in the fact that many chapters have seen particular implants slowly fade or stop working completely.
I have to say, I think it might work out a draw, with the 30k boys having all of the above, but the 40k's have the more modern marks of armour and weaponry.
Id imagine 40k SMs to be the better soldiers. Their faith in the emperor provides them with immense inner strength.
The 30k marines also had great faith in the Emperor as their creator and gene father, and drew strength from his vision for humanity. They just didn't see him as a god.