It's definitely a system shock for people who haven't played in a while or don't have experience with more difficult pokemon games, but I promise it's very doable. Hard pokemon may just not be for you though, so don't force it too much.
The biggest thing for making battles is counters. you can read the full effects of the terrain and work out ways to turn it to your advantage, as well as tune your team to have a better advantage against the leaders type, or even try to counter specific pokemon that are giving you trouble.
For Shelly in particular, one example would be using a pokemon with fake out (say persian for example) to prevent Illumise from setting up the rain, then transform the forest into a burning field with something like flame burst or lava plume. but there's many different pokemon and strategies that work. For what it's worth though, Shelly is generally recognised as one of the hardest leaders relative to the point in the game you fight her at. later on you have much more options to work with.
I'd recommend heading over to the mod market and picking up expscale from Aironfaars mod box, which lets you prevent yourself from going over the level cap, and then multiply your XP gain so that you can easily train up new pokemon to swap in for fights