(especially since the pylon also takes up support slots and cannot garrison)

To the best of my knowledge they CAN garrison? Since there Immobile. Or so I've heard discussed? Zombo?

My one was broken portals being used with no detrimental effect. My solution for that was that a formation that uses a broken portal should gain a BM.

I'm a bit concerned that the new Necron codex will prompt a lot of revision. I'd say it'd be better to just make a new list to represent it (depending on the scale of the changes, of course).

My preferred adjustment is to give the C'Tan the Walker ability. Right now it is a real risk to teleport them into terrain and if the Nightbringer wants to engage an enemy using close combat in terrain, he could lose 1/3 of his DC on the way in. Just not realistic or playable as it is.

I'm also not sure about Destroyers. I don't know what the solution is either. They are so much more expensive than other formations that I struggle to fit them into my army. They have nice abilities and are useful but you can get more bang for your buck with other, cheaper formations.

2: reduce destroyer cost/size and increase their flexibility. at the price, they're very hard to fit into a list because you need, at minimum, a 405 point infantry-unit to be the BTS (unless you think you can win without a BTS left, a 6 point infantry formation is particularly suceptable to breaking when the opponent only needs to break it to get the victory condition. something not suffered by any other army) and while destroyers (and abbatoirs) may be worth their cost, unless the list allows them to be taken without hamstringing yourself in other key areas, their actual value is irrelevant.

1: Lack of Anti-Air capability. it feeds into a much larger list design concern regarding their war-engine allocations getting choked out easily, but the fact that Pylons are the only choice and are so expensive per shot, means that the larger necron warengines rarely ever get taken (and when they do, at significant tactical loss in other areas, as the only options for Supreme Commander and AA fire are also expensive war-engines. If you take an abbatoir at 3000 points, you're stuck with at most a single AA shot and no supreme commander possible)
I'd like to see some non-warengine AA abilities somwhere (my ideal location would be the tomb spyder i believe) so as to free up the reliance on pylons quite so much.

1.5: I'd also like to see the Pylon (and/or the Ctan) moved so they're no longer in the War Engine allocation. (especially since the pylon also takes up support slots and cannot garrisson) its hard enough trying to fit a big thing into the list as it is, especially without cheap/aircraft formations to bulk up the activation count. to be stuck without any serious AA fire or a supreme commander in the process is a real killer.