I don't like that Lightroom's Develop Module is separate from its Library. That really bugs me.

All my Photos are in Lightroom, but apart from the asset management, I can't really think of anything it does that you can't also do in Aperture, albeit in perhaps a different manner. I do recall a few things in Aperture having odd UI however, such as cropping.

Nice additions to Aperture 3 include brushes, mapping integration and face recognition. I'd like to see the last two added to Lightroom. Aperture's method of grabbing GPS information from an imported track looks positively stupid however. You have to drag at least one photo manually to the position on the map at which it was taken. Then it figures out how to place the others. Not sure why you can't just drag it anywhere onto your track and then have the program use only the timestamps for matching all of them.

I'd also really love to see masking abilities in Lightroom similar to how they're implemented in Lightzone. That feature simply rocks for making lighting adjustments in your photographs. Brushes simply don't compare.