Drive bay replaced with built-in 7 hour battery life and SD card reader. If you want more than a 160GB hard drive, either upgrade to $250 or use a FireWire/USB drive (better to have an external anyway for backups in case you lose your laptop).
 Mac OS X integration with wireless network and Bluetooth keyboard is seamless. These days I plug in display, USB hub, and power, and it takes me less than 15 seconds to do especially because the power and display connectors are so small and easy to plug in. If you really need a docking station, there are third party ones.
 Runs Mac, Linux, and Windows XP/Vista. You'll need your older machine for Windows 98, but that's the case for practically any new laptop anyway. Mac OS X is great for development and comes with all the core tools and libraries pre-installed.
Only thing I'd suggest is to add RAM to the MacBook Pro's base 2GB. And I hope you aren't still using floppy drives.
By dual screens, do you mean two external displays or just a secondary display? The MacBook Pro does have dual-link DVI output and can drive quite a few displays, but you'll need an adapter.