We made a few test-calculations and a test run for gym-balancing. While the difference probably becomes less noticable in later stages, in early-game 5 levels make a huge difference. In a test run, Kansa 2HKOd Shellos (which had it's 100 evs put into health), while Shellos did less damage than the leftover-recovery on Vivillion, with a super effective hit (which had no health or defence investment, and is generaly a rather frail mon). Likewise Ninjask did less than 15% damage on a neutral hit, full attack investment (both evs and nature), and was 3HKOd. The difference is just enormous, and I shudder to think what would have been wrought by a Scizor instead.
Gyms are meant to be not too challenging, and should be generaly accessible to most teams, not only those who were lucky to have the fitting 4times effective moves or something of the sort. It's for fun afterall (unlike team mal HQ and elite 4, those should go all out).
Thus, at least for the start until 5-level difference doesn't make such a big difference anymore, the signature pokemon will be on the same level as the player pokemons, others 3 levels lower. This is subject to change in later stages of the game, when bigger teams mean a wider variety of choices to battle situations and higher levels make 5 level difference less significant.
Everyone should keep in mind, when building his team, to make it for fun, rather than winning or actively blocking competition from important moves and items. The gyms are a fun add-on, the competition is in the direct battles
You can directly see the difference of 5 levels in the following replay - where Ninjask was 3HKOd before, it now even takes a critical hit and survives long enough for fury-cutter to kick in. In another test-run, it was also checked how it would fare against Shellos, and while Shellos still lost, at least Vivillion was unable to out-heal super effective hits with just leftovers, and didn't 2HKO shellos (which is a tank afterall).
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Akroma approached the first of her many trials yet to come. The domicile of the Butterfly-Queen, one of those legendary, queen-type pokemon, and the cowardly human who had bound her to her service by vile magic (what else are pokeballs if not vile magic?). The diviners had foretold that, should she be able to overcome the Butterfly-Queen in battle, she would bestow great power upon her...she must not fail...
The domicile was hidden from view, a hidden garden built on top of the highest building in the city. The swarm of butterfly servants was so thick, they cast a constant, multi-colored shade upon the garden, and the trees made sounds like wind chimes, hanging so thick with coccoons...
The battle was brutalThe ButterflyQueen was struggling with everything she had (which was mostly struggle bug - perhaps nomen est omen?), while Alma Elma, playfully, almost sadistcaly held back her power - at first. With every strike, she cut deeper, going faster and faster, to the queens despair. The bug badge was bought with blood.
The price that was claimed was an ancient toxin. A poison so potent, it had been hidden away for decades - now in Akroma's hands. TM6: Toxic