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What is the best? Well I'd say that's a Ford vs Chevy, Apples or Oranges question. A quality rig, whether it be standard or reverse flow, can't be beat.
I would say that it is up to you. Reverse Flow's also have a radiant heat aspect that isn't true so much with tuning plates. You will have to relocate the stacks for RF. The plate will be be and easy install. Tuning plates will be trial and error to some degree. You may have to make several attempts before finding what will work best.
My preference would be RF. If you build from scratch, consider a down draft design.