Posted my Necron PDF (it's nice having an 8 page one for a change....)
Anyways, as I was going through it I noticed several rule issues that needed solving. So I'll tell you each individual change and discuss them. You can argue against if you like, and I'll likely change it.
All Reactive armor saves changed to 4+:
This is kinda funny, because it will never give a Necron any reason to brace against weapons batteries. However this seemed like the best solution to fix the shroud/escort issue.
Lightning arcs no longer ignore holofields:
Necrons pretty much always win against eldar. So this was axed. Someone tell me why the Eldar would design their defenses not to work against the enemy they've had since the beginning of time? Note that gauss whips still ignore holofields on rolls of 6. (however that one makes less sense, but it's there for simplicity of rules)
Removal of escort portal limitations.
Why not?
Alteration of VP rules:
So escorts no longer count as always crippled (where did they get that idea?) and instead do vps like other necron ships. I.e. if healthy they only count as 10% when disengaging, if they took damage (any) then they count as 25%, if they are crippled then 50%, and if they are destroyed 150% (as they can't leave hulks)
Capital ships work exactly the same except they can leave hulks and those count as 200% vps.
The reasons for this is that if a necron ship was destroyed it would be almost an automatic win for the other side. With less harsh VP rules CLs would be more viable (as they are the only ones who generally get hulked)
Alteration of costs
Of course the reaper and cartouche were added (to make the list have more than 5 options...). Both their costs were increased slightly to represent the 4+ save they were getting.
The Scythe was increased more significantly (because of the 4+ save) and also because of how renown they are as being better than tombships. With this increase they shouldn't be as good comparatively.
Revision of fleet list:
Necrons suffered from something I like to call 'floating points'. As they could buy Re-rolls that weren't attached to any ship, they couldn't be won by their opponent. Necrons also had no fleet-commander, something fundamental to the game itself. 
So I decided to change the Sepulcher into the fleet commander equivalent. The player must take a sepulcher if he has any capital ships (sensible, as opposed to 750 points) and it must be on the largest vessel. 
Then the re-rolls are linked to the sepulcher. 
With this hopefully it will counteract the VP revisions slightly. 
Tombships for every 2 cruisers, not for every scythe, this makes more sense, and makes a more versatile fleet. Also it limits the number of larger ships that a player could take (as with the addition of the reaper, one could have 2 large vessels for two cruisers). 
Light Cruisers limited to 6 between them; I understand the fluff reasons for there not being 6 shrouds around, but really... who would do that? I like this better than the limitation of 0-3 shrouds and 0-3 cartouches. As that limitation seemed... well... stupid.
Escorts now just limited to 24 per fleet. No real good reason to make sure that you have max 12 of each.
Anyways, feel free to comment. I know people think Necrons are a bit OP, but the effective things increased in cost.