Visual Studio Integration
It would be very helpful if it would be possible to edit master pages and page layouts in VS2005.
It would be groundbreaking if you could run a little instance of MOSS 2007 on a local machine (e.g. in Cassini) to debug and develop your WebParts. This "little instance" should connect to your MOSS 2007 content database. I bet this will come with one of the next MOSS releases or service packs?!? (If I would be jobless I would implement this or a similar thing and make a lot of money)
Variations
Let's say you have three different page layouts and only one content type (all page layouts use the same content type). This makes sense because you are not sure which layout to use or you want to give your authors the possibility to switch between page layouts (what only works between page layouts with the same content type).
If you now create a variation of a page using one of these page layouts (or let MOSS created this variation automatically), SharePoint 2007 allocates the first page layout you created with the content type to your new page. This is wrong in 66% of all cases (for three page layouts), so you probably have to assign the right page layout by hand. Not funny in ECMS environments with more than one language variation. But we heard about this as a feature.
Separation Of Content And Structure
Separating content like images, text, etc from structure (navigation tree, site structure, master pages, page layouts, css, ...) would allow you to implement redesigns easier and to enable parallel work between developers and authors.
If you developed a large scale enterprise website with daily new content, and, on the other side, plan a redesign with seriously impact on the structure, you have no other possibility as implementing your redesign on one system (let's say staging environment) and to maintain your content on the other system (let's say authoring environment).
What you have to do now is to maintain your content on both systems (authoring and staging). This can be very hard. Another possibility would be to automatically deploy your content from authoring to staging, but this is no out of the box functionality and I'm sure it's not easy to implement.
Partially the separation seems to work if you are not provisioning publishing features and if you don't use SharePoint Designer. At least master pages are stored in the filesystem for that case.
Deployment with the integrated deployment path...
... should work (without re-setting master pages or breaking sites). Hope there will be a hotfix soon.
SharePoint Designer...
... should not freeze the whole system, double html headers or reformat your well formatted html code.
... to be continued.