Is there any reason why I can't run #12 throughout my shop and run all circuits (even lighting) on 20 amp breakers?

I would use all #12 and 20 amp breakers. Some will say you can save money and use #14. I wouldn't.

I already have 2 rolls of #12 (1000 ft) at no cost, I bartered for it. My main question is putting the lighting circuit on a 20 amp breaker instead of a 15 amp. I purchased all 20 amp breakers.
Bob

You can, and I would. It would cost more money for you to downsize.
#12 all the way is fine. I hate #14, especially in romex, not an easy upgrade later.

This is an old argument, but using #14 for lighting is NOT a "downgrade". In a residence, there are many reasons in favor of using #14 for lighting and not that many in favor of it.
"Saving money" is the knee-jerk answer to those opposed to it. This is RARELY the case.
Those in favor of it are typically in the bigger/more is better camp.

Here is a recent thread on this very subject:
https://www.askmehelpdesk.com/electrical-lighting/big-basement-project-electrical-diagram-195654-2.html

FWIW: You can put a 15A or a 20A breaker on #12 wire. You cannot put a 20A breaker on #14 wire.

It's not the question you asked, but I think the above is worth mentioning.

The breaker must first protect the wiring and then the load. Connection terminals have wire size limits and number of connections to the terminals. e.g. A breaker is allowed only one wire to it's terminal, but multiple circuits can be pigtailed.

Please remember he has #12 and 20 Amp breakers, using #14 or 15 Amp cost money.
Plus evryone here knows I am a #12 person.
In addition to above mentioned, 20 Amp is more capable, you can do less with 14 amp.
PLEASE, If any one can tell him a downside of using #12 and 20 Amp that he already has, please let me know.