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It's really easy to be largely underlevelled for the Johto Elite 4 because of the really low level wild Pokemon. I find that I'm always around lv40-42 with my team when entering. The Elite 4 of Johto is easy anyway, so you can defeat them with ease even at that level.
If you head to the Johto safari park, you come in a cave where you can go up and down. If you go down, you come across water and two waterfalls. Climb up the first waterfall and you come across a patches of grass with really strong pokemon from lvl 30 to lvl 40. These also pokemon that give off a lot of XP like tauros, miltank etc. It helped me a lot in training.
I have a thing about grinding like crazy before all Gym Leaders and E4 members, so I've never encountered this issue, fortunately. Also, I never battle anyone unless I know precisely what critters they have and at which levels because I'm a massive wimp when it comes to stuff like that. So the Johto E4 weren't really a surprise. (Added to the fact that I could remember a lot about them from Gen II.)
I found that I was one or two levels under the Champion, which is pretty good in my opinion. I tend to grind before the elite four , but do hardly anything before gym leaders. Overall, I did pretty mediocre, and although I had to use a lot of revives, I did beat the Champion.
I think it is intended that you are underleveled for the elite four, so that you have to level up, and may as a result, go back and do whatever little side things you missed. Even if you just grind it extends the overall main game time.
I was slightly underleveled as well, I didn't even have a Pokemon with Ice type attacks to take down Lance so it was a real pain to try and take those dragons out...
Most, if not all the time, I'm underleveled for the Elite Four. The reason being is because I haaaate grinding, and I have a habit of avoiding grass when I don't need to go through it or anything. I've tried to rid of this several times, to no prevail. For my Platinum, I actually bothered to grind a bit, after realizing just how underleveled (about 15 levels or so) I was compared to the Elite Four.
I find this with DPPt. Those are the only games I play with a team consisting of less than 6 Pokémon (usually 4) because I just don't feel like reaching the league at level 50 when Pokémon I'm facing are up to 60.
I'm pretty sure the developers made it that way so you would have to get a certain amount of gameplay out of the game instead of just speeding through the game. anyway i love to go back and fill up my pokedex while gaining XP along the way and leveling up my pokemon:)
The only game I didn't have that problem in was HG/SS haha. I honestly never tried to get my Pokemon on par with gym leaders, and they were ever really a problem for me. But once I got to the Elite Four, having to battle five Elites in a row, all 20~ levels above me... yeah that's kinda tough.
But yeah, like I said, HG/SS was the only one that didn't give me problems.
I would have had an insanely difficult time trying to beat them... except.
I managed to get Entei and Raikou. With Raikou, I taught him Thunder to weaken Lugia til I caught him. When I got Lugia, I taught him Blizzard just to take down Lance's dragons. The three of them alone took down the Elite Four for me.
To me, the Elite Four was a breeze. All of my Pokemon were above Lance's Level 50 Dragonite by around 5. I never ran away from trainers, and I always loved to explore the caves. You should train all your Pokemon up Wonderfulpat. Use the EXP. Share. My Typhlosion was always my strongest Pokemon by around 5 levels.
Yeah I can say that I have been faced with the situation where my pokemon are lower-level than the Elite Four's, but nothing a bit of grinding will fix up, plus I find actually, having your Pokemons' levels a tad lower much of a challenge and personally, its more enjoyable that way for me.@Tombo, between what? Pikachu. XD;
I can tell you i grind ALOT so i never really have this problem. Although back in the day playing emerald and to this day i find the hoenn leauge quite damm good. Drake or whatever his name is was tough!