Aside from the spawn system, i wouldn't really recognize these as flaws.
Weapon damage has remained consistent across 4.1 and 4.2, the only thing that's been adjusted is the accuracy of a few weapons and the invulnerability time. The main thing in play is the invurn time, as it is now possible to kill someone much faster with weapons like the dd44 and P90. While i think other second tier weapons like the autoshotty could use a slight buff to compensate for the new instant death P90, i find the invurn time adjustment to overall be a positive change as it corrects a few critical gameplay issues that you seem to have considered features.
With the changes, i've had a much easier time dealing with people who like to sit on top of an armor vest, and then spam the entire hallway when someone tries to pass by them. While the invurn time means they could arguably kill me faster, their refusal to aim means they'll be doing damage at a somewhat slower rate than i would. If their crosshair happens to pass over my head once every second or so, they would still have a good change of comming out on top in 4.1. In 4.2, however, i would have a good chance of winning the fight even without armor if i consistently tracked them.
So, yes, it initially seems like a step towards an unpro GE:S, but it's actually the opposite. You can no longer remain alive just by crouching on top of an armor vest and spamming your silver PP7; now you need to be more intelligent about who you engage and how many times you hit them within the second. Weapons like the CMAG are no longer as potent, but now it's possible to do just as well with weapons like the PP7.
Anyway, I've noticed that oddity with the spawning system as well; it seems like it's rather fond of placing people in the exact same spawn i came from 2 seconds ago. But don't worry, we're looking into it.