Let's get a few things straight here...
(GBA) Advance Wars
(GBA) Advance Wars 2 (might as well have been Advance Wars 1.5)
(NDS) Advance Wars Dual Strike (AKA Advance Wars 3 for NDS)
(NDS) Advance Wars Days of Ruin (could be loosely considered Advance Wars 4, but it's different enough in story, unit types, unit abilities, and COs that it's a stand alone Advance Wars)
All that being said, I'd say if you're playing GBA, get Advance Wars 2. If you're playing NDS, either Dual Strike or Days of Ruin are good choices. If you were to never have played either and saw each of them played side-by-side, I'd say your decision might boil down to personal taste of the themes. I personally prefer DoR for it's darker theme and exceedingly better soundtrack. I'll never say that DS or DoR is overall better than the other. They are equally superb games, each with their own pros and cons. Obviously, the addition of NintendoWiFi battles sets DoR ahead of DS, but only for that reason. Saying DoR is a better game for only that reason is hardly fair to Dual Strike, which offsets DoR with more content.