The one major problem I can see is with the Rura Penthe scenes.

Somehow (probably explained in the comic but not on screen) Nero had out fitted his mining vessel with advanced weapons.

That has to stay if the attack on the USS Kelvin is going to make sense.

So what happens to his ship while Nero is in prison?

Surely the Klingons would have dragged it off to their version of Area 51.

If Nero's ship was just a mining ship they could feasibly have used it to help with the dilithium mining on the planet but seeing as it has advanced drive and weapon systems I can't see the Empire just parking the thing in orbit around the planet they are holding their Romulan prisoners on.

Another problem is if Nero's ship is in Klingon space when it arrives, why is the Kelvin there?

It's a shame because it was a major sequence with some nice touches (like the leather helmets hiding the Klingon's shameful resemblance to Humans).

Remember the ship hasn't got the Red Matter yet so if Nero isn't captured he would need to keep his head down.

He took out the Starfleet task force but he wouldn't be able to hold out that long against a major fleet attack if he stirred up too much trouble too early (his ship is big and well armed but it's not a Borg cube, one ship managed to do enough damage to seriously disable it).