Now that they're heading in the direction of supporting academics by introducing endnote support, I'd like to see more movement in that direction. Figure numbering, table numbering, list numbering, list of these things like a table of contents, cross linking references in the text.
I'd also like to see Numbers get more compatibility with unusual file types like tab delimited text files. Currently I have to copy and paste these in and out of a text editor to get them to work. Generally, the improvements from Numbers 1.0 to Numbers 2.0 have been impressive, but I expect to see vast improvements again in Numbers 3.0.
Keynote is brilliant the way it is. It trounces PowerPoint on nearly every level. I would like to see more support for flow diagrams and connectivity between objects like you get in PowerPoint however.
These would make a killer suite of applications - something we nearly have - I use iWork over Office whenever it's capable (which is rarely when comparing Numbers to Excel but I never use Word or PowerPoint any more).