DIP Alternative To ATMEGA16U2-MU(R)
There's not an equivalent of the ATmega16U2 in a DIP package but one common way to adapt SMT parts to a DIP package is via an SMT prototyping adapter. There are quite a few companies that manufacture such adapters but here's an example product from a company that will also solder any parts available from Digikey onto the adapter if you're not confident on the soldering side of things:

TQFP-32 to DIP-32 SMT Adapter (0.5 mm pitch, 5 x 5 mm body)

But taking a step back on your project if you're prepared to do a little extra work there are a few different ways you could go about programming an ATmega328 without using a seperate microcontroller for the sake of in-system programming:


You've mentioned being able to change the bootloader itself but really once "fully sorted" you shouldn't need to change it often, so maybe you could write a serial bootloader and use one of the FTDI serial to USB chips or pre-made adapter leads (some come with 0.1" connectors). That would also cover basic serial communication over USB.
You could use the ICSP interface for initial bootloader programming and a device such as the AVR Dragon that can do high-voltage programming. It also has some nice debugging features that will be useful during initial development. 
Another option for initial programming of the bootloader when using a DIP package is simply loading your own bootloader by plugging it into the Uno before transplanting the chip into your own design.


Atmel have some example bootloader projects and while it may seem onerous at first sometimes rolling your own is the best solution and gives a lot of insight into how things work behind the scenes. Otherwise there are some open source AVR bootloader projects that include both the firmware and PC side of things that may be a good starting point.