Raimon City Ferris Wheel Battles, Raimon City Sports Arena Battles, Hodomoe City Heart Scales, Souryuu City Triple Battles, Yaguruma Forest Star Pieces, Hiun City Ice Cream Shop, Hiun City Massages, Hiun City Berry Clown, Sekka City Happiness Checker, Fukiyose City Move Deleter, Fukiyose City Move Releaner, etc.
As you can see, there are tons of reasons to use Fly to go back to older locations within Unova, even before you defeat N and Geechisu at the Pokemon League.
I find it interesting that nothing you've said really compels me to always have a Fly user in my team (
except for the Move Relearner, but I'd go there only once or twice and I could go walking lol). You don't need to backtrack to Raimon/Souryuu only to train your pokémon, as I said, I'd only need the move Relearner a couple times, the Ice Cream Shop sells... ice creams... and I didn't use to constantly backtrack to Route 39 in HGSS/GSC only to buy Moomoo Milk, why would I need berries if I have Dream World which is much more efficient and varied, why would I need to constantly check/increase my pokémon's happiness, why would I need to constantly delete HMs from my pokémon...
Don't get me wrong, I could have a Fly pokémon in my team and visit all those places... But only after E4. Before that, as interesting and fascinating and varied and blahblah Isshu is, I see no reason to backtrack all the time if my main objetive is always go forth, training and getting badges and foiling Plasmas and catching new pokémon. The breeding, the grinding, the item collecting, the happiness increase, the moveset building, all of this I leave to do after E4, as my team members are strong enough to solo the region alone or in a reduced number while I do whatever else I want with the other teamslots.
Also, Meraruba should evolve in an earlier level. I'd love to have one in my pre-E4 team with Fly (and Flame Body for post-E4 breeding!), but it evolves only at lv59, what the f
uck. I could work around it if it evolved at lv54, but 59 is too much...