I am doing the storylines right now (Unova is done, I am at the beginning of Hoenn) and yes it is harder than the original games but it's far from impossible. I didn't used a single healing item in Unova and only got beated once or twice around Castelia City and i'm far from being a great Pokemon player.
You only need a team with different types know which types are the most effectives against which. My Unova team was Krookodile, Darmanitan, Archeops, Cofagrigus, Galvantula & Mienshao. I decided to not use my starter anymore when I got to Castelia and replaced it with Darmanitan. All those pokemons have a neutral or at least not a bad nature like Modest on a Krookodile and IVs 15+ on needed stats, so nothing hard to get. You should also train until you reach the level cap before battling a gym leader.
Since you are in Hoenn, here is the team I chose. If you want help building one, feel free to contact me.
Swampert • Gardevoir • Hariyama • Manectric • Roserade • Flygon