As in, get the balcony Neo was on at the Merv Palace. Plus more floors and useable weaponry. Be cool to have a sword on the wall and take that s.o.b down and go swingin and choppin on someone. 
Put a version of the White Room in the Machine Construct..and maybe some 255s (or agents with names)walking around and you can try to break thier shield if you think you can take one..and possibly have a glimpse of the Machine City where the pods are
And for Zion...redo it alll together..here's an Idea..1 floor dojo, next floor nothing but weapons, next floor hovercraft docking station
Since the Cypherites and EPN have established a name for themselves...make one for each of those orgs..
Make a shrine of Cypher for the Cyphs
Make a shrine of Neo in EPN's construct
make cars driveable, make helicopters blowup, make a way where we can walk into every floor of every building with thier being no mission, put in crotchrockets, put in a single white hall way with it leading to a special door, like a new construct or even through the Ascension Monument..Make swords useable, create different weapons, like a mace, grenades, ect..Make a new constuct where its nothing but trying to fight high level sentinels in ones own hovercraft..Last but not least, make it to where we can jump outta windows with shattering glass everywhere (when I think of more I'll put it in here but those are ideas that just kinda popped into my head)
and that pretty much sums that one up..
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