Note: Don't complain if you have to spend hours grinding, or if you need to read this entire thing AND grind for hours, because your team has a ways to go if you want to be the champ and best Steven in a fight.
Also, read this entire thing for best results.
Right now you don't have any Pokemon with super effective moves against Winona. You need a good ice type, rock type, or electric type for that. As First Sinner said, you could go with Gyrados by spamming dragon dance and mindlessly clicking waterfall/aqua tail. Unfortunatly, this only works if you dragon dance enough, as half of Winona's team resists water moves. You could run ice fang, I guess, but thaty's only for Swellow and Altaria. Skarmory can go down to waterfall/aqua tail, so you shouldn't worry about that. Esentially saying, you should train up a Gyrados for Winona, but train up some other Pokemon as well so that you still have a chance in case Gyrados faints.
You're set for mossdeep with Marshtomp, Trapinch, and Breloom. Watch out for Solrock's solar beam, though, so take that one out first. Extra assurance? Use that Gyrados I wanted you to train up for Winona's gym.
You might be able to take Wallace, but he has some ice moves up his sleve. Don't just rely on your Breloom. Use
your other Pokemon to soften him up, then bring in your grass types and wipe him out. For your grass types, I would suggest using Breloom(as you already have it), Ludicolo(ice is neutral), and if you want, you could go for Shiftry. Still, Milotic will probably outspeed, so go for a Manectric or something if you're still scared.
For Sidney, you're I'de suggest your Brellom, as well as a solid bug type for max damage. I would not suggest either Ninjask or Shedinja, because they are both too frail and one is part ghost type. Breloom will do against Sharpedo, but Absol will tear a hole in your team if you don't have any fairy types. Train up a Mawile, as well as a Pincer or an Armaldo, and you should be set. Just make sure to stack up on those speed EVs!
Unless you remodel almost YOU'RE ENTIRE TEAM for the second E4 battle, Phoebe will be extremely aggravating and annoying. Train up some that Mawile you just got some more, and snag some decent dark types if you can. I would go for Sharpedo, but switch out for the first Banette! It has will-O-Wisp. which effectivly cripples Sharpedo. An Absol will do as well. Take one or two fully evolved(or in the case of Dusknoir, where you have to trade for it, an eviolite Dusclops will do) ghost type Pokemon and you will do fine. Just keep your Swampert in the team, we don't want it to feel bitter, do we?
Train up your Numel for Glacia. If you want to be extra secure, teach the Armaldo you used for Sidney a good rock type move, train it up a little, and watch it go! Still, Armaldo should go down SOMETIME, right? Use an Aggron for best results. Surprisingly, Breloom should do fine with those fighting type moves, going against Walrein. The other Pokemon I listed all have weaknesses to water, and that's the problem. So use your Breloom and you'll do just fine. Don't forget to grind, though! You don't want to lose to the third member of the E4 and start again, after all your hard work!
It's time to become a temporary architect! Dig your Gyrados out of the PC bo you threw it in for Drake. All his Pokemon exept for Kingdra should fall to ice fang easily. Set up with one dragon dance and sweep. All this should be good, exept for the fact that that Kingrda is gonna be, well, annoying, with an ice move. If you want, go ahead, mega evolve your Gyrados. More help? Concider using Walrein or Glalie. Just make sure they both have good/decent ice moves. Give Glalie freeze dry for Kingra, grind a bit, and you're set!
Last but not least, it's time. To. Fight. The strongest trainer in the entire Hoenn region... Steven! Let's just hope you win on the first try, or it's back to square one! Scarmory should lose to your Camerupt, and Camerulpt should do fine with Aggron too. Use Camerupt against Metagross too, assuming it lives, and use that Walrein you used for Drake for Steven's other Pokemon. Just teach Walrein surf or something. Snag a Torkal as well for Metagross. Use Breloom as an altrenative to Camrulpt, actually, save Camrulpt for Metagross and tackle Aggron with Breloom! Mega evolve Camrulpt if you want to, but I was thinking of Mega evolving your Absol after teaching it a good dark move, because Metagross is part phychic type.
I know you didn't ask for a walkthrough of the gym leaders or the E4 and the champ, but I hope this helped!
PS: I hope this didn't fry your brain!