I've only been using LR for about a week and my first copy was 2.0, so I may have some of this wrong.
I do think LR needs better integration at the file level. Yes, the database method is best, but only if you also allow file manipulation at the file level. There is no batch rename as there is in Bridge. Nor is there integration with Photoshop tool, like Image Processor.
Also, I think it would increase the tools effectiveness to allow file level manipulation for zooming. Having set zoom points is aggravating.
Nor can you move and rename folders in LR, since it's working off a catalog file, not the file/folder level.
LR cost 1/3 what PS does. Is it asking too much to have file level capability? It would be nice to have LR use images that are available and then update the catalog when you close or while open, in the background.
In short, I'd like to see better file level/Photoshop integration. It seems like now I have three programs always open, PS, LR, and Bridge.
Or, as an alternative, I'd go for Bridge plus a catalog option to categorize and view images, like LR. Change ACR to show dual up before and after shots and that would be nice. Allow ACR to remain loaded while working in bridge for immediate edits at the RAW level. ACR REALLY needs a dual pane, before and after.
I'd also like to see a way to set defaults, such as Set Sharpening to 0 made simple.
A dialog box with setting would be nice. Save settings, Done. LR then automatically uses those settings with all current catalog images--such as set sharpening to 0.