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RD has better gameplay in a given chapter, but it forces you to largely play chapters the same way all the time, ie not a whole lot of choice for unit selection (I'd go into more detail, but I don't want to spoil anything for you. You'll see what I mean when you play it), while SS has the best gameplay of the GBA FEs, though not as good as RD, but with a few exceptions, IMO the chapters aren't as interesting as FE7, or RD for that matter, but it's more of a classical FE, as in free to use whom you want. As for story, I'm not a big fan of either, so pick what you want.
"You know, Hobbes, sometimes I think the surest sign that there is intelligent life out there is that it hasn't contacted us." - Calvin
I'd say Sacred Stones. Radiant Dawn bothers me with its non-linear chapters. It's not a story problem as much as it is a gameplay problem... Whereas you can choose to level any character in Sacred Stones (even in hard mode), characters in Radiant Dawn are just left behind, and there's no way to catch them up with certain characters. There's also a huge problem in class balancing...