My big complaints on the TA are the extra 800 miles because it wanders all over the northwest, and the previous remark on Virginia. Why do we have to go to Missoula, it's not bloody Mecca. Why do we have to zigzag south then north then south to traverse Hells Canyon?
There are many, many, many, many places on the TransAm where you can cut off miles or hills. If you ask Google maps for a route from Yorktown to Astoria, it will tell you that it's only 3012 miles. Why would anybody want to ride the extra 1200 miles?
I understand that many people have time constraints, work or family or something else. They really don't have enough time to comfortably do 4215 miles. Those people have to make compromises, but they get to choose the compromises. Compromises, however, have costs, and you have to decide whether or not you accept those costs.
Ask yourself why you want to ride across the country. If it's to check a box, then make all the compromises you need to, and get it done. But if it's to have fun, then try not to make too many compromises. Maybe you'd prefer to choose a route that is shorter but doesn't go all the way across the country. Or maybe wait until you do have enough time. Or maybe you decide that your constraints can be bent.
In my opinion, and this is just my opinion, if you have enough time, stay on the route. Yes, it's harder and longer and hillier, but it will be more fun. The shortest route is to just stay on the couch.