You start in Littleroot Town, get your starter, and all that stuff. Then, you head straight for Petalburg City, where you witness the game's evil team(s), either Team Magma/Team Aqua or a new team that uses their resources to reawaken Groudon/Kyogre for whatever reason (I have no idea what to do with this game's storyline, TBH), but quickly escapes to Rt. 103. You follow them there, and you cross the water through a recently built footbridge (which allows you onto the east side of Rt. 103, but Rt. 110 would be blocked). You then follow them into Altering Cave (or some new cave which takes its place), and defeat them. After that, you can go back to Petalburg City and challenge Norman for your first gym badge (his roster would consist of Zigzagoon and Slakoth, maybe some better early game Normal types if they're available). You could possibly catch Fighting types in Altering Cave to help you with this battle). From there, you continue to Rt. 104 and through Petalburg Woods to Rustboro City like in RS1. You can challenge Roxanne for your second gym badge (possible roster: Geodude, Aron, and Nosepass).
From here, you would not sail to Dewford like you did in RS1, as Mr. Briney will no longer take you there (you cannot reach Dewford in this game until you learn Surf). Instead, you would go through Rusturf Tunnel and continue eastward until you reach Mauville City. Wattson has retired, and the gym leader that took his place is busy in New Mauville. You can also get a Bike here, but for now it's only a normal Bike (you can upgrade them to get Mach Bike and Acro Bike functionality later, instead of having to switch bikes). Instead, continue north on Rt. 111, and then east to Rt. 112. Mt. Chimney and Fiery Path are blocked off for now (either Team Magma or the new evil team is using Mt. Chimney as a base, and you won't be able to explore it until much later. Furthermore, Fiery Path, Mt. Chimney, and Magma Hideout are all connected now, so you explore them all in one go). Instead, a new path has been built so you can simply walk up to Lavaridge Town, and challenge Flannery for your 3rd badge (possible team: Slugma, Numel, and Vulpix). Eventually (I'm unsure whether or not you should head north to Fallarbor Town at this point), you head back and proceed to Slateport City (which you could've accessed as soon as you reach Mauville City, but there'd be little of interest there until this point). You fight the evil team again in Slateport, and obtain Surf when you defeat them (you can also upgrade to the Mach Bike by this point). From here, you have two new gyms open that you could do in either order. The suggested order would be to go back to New Mauville and help out the new gym leader there, after which you can go back and challenge him or her (possible team: Raichu, Magneton, Electrode, and Manectric). Your other option would be to Surf from Rt. 109 all the way to Dewford Town and challenge Brawly (possible team: Machoke, Medicham, and Hariyama).
After you have the first 5 gym badges, you can take the S.S. Aqua to Lilycove City (Rt. 119 would be blocked until you come from Fortree City), and then you need to work your way towards Fortree City and fight Winona for your 6th badge (possible team: Skarmory, Swellow, Altaria, and something else). After that, you can go back to Lilycove City, and explore the remaining areas in a similar manner to RSE (in terms of gym teams, Tate and Liza would now have Solrock/Lunatone and Gallade/Gardevoir, and Juan would have a bunch of new water types).