Emp
This is just stupid, but I was watching Reloaded again and when it came time for the Neb to explode I wondered why they just didn't use the EMP on the bomb. It's electrical, we see it fly by itself before blowing the Neb up. Again this is just something stupid that I noticed, but hey maybe some of you will have something to say here.
This is what I think could have been done. They use the EMP on the bomb and the Squiddies would come after them and the Hammer would arive and EMP them. Then the Neb would still exist and be used in the Zion fight and Niobe would still have to give up her ship. The only big change would be no " I have dreamt a dream, but now that dream is gone from me." Oh well. Anybody?