Is there a way to make wiring a bare microprocessor to a shield easier?
You can make adapter boards (one for each mcu model).

The bottom side (male headers) would plug to the breadboard and the upper side would have female headers with the same pinout as an Arduino board (female hearers placed in the appropriate positions to match Arduino shields).

Such a board shouldn't be difficult to design.

Here is an image that resembles what I describe



It would adapt the pinout of a bare AVR to the pinout of a typical Arduino so that shields can by directly plugged on top of it.



Also a pinout diagram may come handy to speedup things when you use a bare chip with Arduino code.
(image source)


Another similar solution is a small printed sticker placed on top of the AVR
(image source)