Certainly it would be more effective for certain things like shiny hunting/etc, but you would also lose some of the 'comfy' factor in it being slow when you *choose* to do it that way, as it is right now you have a few seconds to do other things between.
Honestly some of the things in the game are so slow/repetitive that I can read a book while doing them, basically being a bot isn't fun, basically being a slow bot is even less fun.
When you see a problem like this come up repeatedly(as often as I'm sure this one does), it's usually a good indication in a game that something is wrong, it might not meed that you need to directly change this, but you probably need to look at it more than just 'farm faster', 'end story mode faster', etc. As long as it's not paid (Which is probably not the actual intention of OP, but instead a 'concession' he thought would be smart) it's an even playing field for everyone. Would it change the economy? A bit for a short while, but it would rebalance.
Given that /who and other similar commands aren't available so it's hard to see how many are on at a time I honestly can't tell if bots are a thing in this game, but if they are this would influence bots a *huge* deal and make them way way overperform, but for regular players it wouldn't be as huge of an effect.
Ironically, the biggest effect would be things that PokeMMO changed for 'balance' in making certain held items consumable because you would get more bang for your buck per amulet coin/lucky egg/etc.
In the end this is no different than saying "The guy farming tentacruels with a X pokemon is way faster than me because I picked a Krookodile with Moxie/EQ so I have to sit through Super Effective/Moxie text each time!". It's a choice we made in what we used, the only difference is one is the pokemon and the other is a toggle. Sitting through Super Effective/Moxie text for *every* hit in a horde is honestly disgusting, and I can sympathize with OP very much so because of it. If I could at least A spam my way through it, it would be tolerable, but having to literally wait for the text to go through is truly a snorefest.
Of course I'm sure this won't change, minds have been made up on this matter long ago, but it would be a huge QoL to at least some players, and it wouldn't effect PvP anyway as you could just force it off in PvP, or you have to wait for the other guy anyway.