I once went to Wake first, thinking that when i defeated him, pokemon below lv.60 would obey me, i didn't realise you had to beat 4 gyms to do that. So, to use my lv.35 Electabuzz,i just wasted all pp on every move cept Thunderpunch. Healed it with potions, then went to Pastoria. That way all it could do was disobey or use Thunderpunch.And, true to Electabuzz nature, being violent, it attacked. I beat 2 gyms without healing. Other than that, i do proper order.
Well, except for on LeafGreen, i always leave Sabrina til 2nd last.
In Hoenn i do them normal order, and when i get Hg/Ss, i'm doing them normal order, coz i've never played Johto before