Here's my take and then my recommendation.
Capitol Hill - The Judge, The Legislator, and the Senator are all fantastic. I personally prefer the Senator of all the RTJ courses in the state and it is the only one that holds a regular tournament ... the Symmetra Tour. Great amenities nearby. They are sticklers here for pacing and use marshals to keep you on pace, so be prepared for that.
Birmingham - Oxmoor Valley and Ross Bridge both take advantage of the best terrain in the state for golf. Ross Bridge is the PREMIER course on the trail and simply outstanding. You can't go wrong playing these three.
Mobile - You can play Magnolia Grove (which used to hold a Champions Tour event) AND ... Lakewood, which is an older Perry Maxwell design, but one of my favorite courses to play. Magnolia Grove though, struggles with handling rain, so be careful about playing in the summer. Lakewood is a great track and usually hosts USGA events, and it's a great vibe as well.
Grand National - this is where I usually play. The Lake Course used to host the Barbasol Champiohship, but the course gets too much play now to host tournaments. The Lakes and the Links course are both great, almost always in great condition. The Links course was recently renovated, the Par 3 short course is currently under renovation (to re-open in October).
The other courses ... if you are in the area, fine. If not, I wouldn't drive out of the way. Robert Rulewich designed almost all the courses and other than terrain, the designs are similar. Very challenging at the green and will defend par with the putting surface.
If it is your only visit, I would recommend playing all 3 of the Capitol Hill courses or 2 plus Ross Bridge. Capitol Hill and Birmingham are so close that you can easily do this. Grand National is super convenient to Atlanta airport and if you wanted, you could do Grand National (both courses) and then drive to Prattville and play the Senator without changing hotel. Plus, a cool college town.
Hope this helps. The Trail is awesome, I highly recommend. PM me or call me if you need more.