The Lonely Mudkip (frame 3252) is an alternative Mudkip we can go for instead of the Naughty one (frame 1026). There are many reasons as to why we would want to do this (also why we wouldn't want to), so I will go through the pros and cons to this decision:

Pro #1: higher attack
This Mudkip has perfect attack (31 ivs + nature) compared to the 23 of the original one. This allows us to hit many, many ranges more consistently, go for different strategies (some more aggressive but far faster) or go for strategies that were simply impossible prior, such as killing Tropius in Winona's gym with Swampert compared to letting Castform finish him off.

Pro #2 safer in some fights

Thanks to our higher attack, we no longer have to risk dying to Rival 3 (6% prior), missing the Shelly range in the Weather Insititute (88% to 100%), or risk another turn against Tate and Liza (the fight lasts for one turn less because we can skip an X Speed due to our very specifif speed stat, which allows us to outspeed Solrock and Lunatone, but not Claydol). The Norman split is also shockingly better: Swellow tends to put you in Focus Punch range for Spinda, and since our higher attack allows us to lead Strength against it, the fight is much safer. The Zangoose also goes from a 65% to a 81% range!

Pro #3 higher special attack

By having 31 special attack instead of 30, Magnemite is no longer a range in Torrent, Shelly, as mentioned, isn't a range either, and Xatu in Fortree Gym is a better range.

Pro #4 much higher special defense
Since we no longer have a minus nature, fights such as Rival 2 or Flannery benefit from this fact. You will basically never have to potion in the middle of the fight (REALLY slow outcome), and Flannery becomes safer, also because her Camerupt is no longer a range.

Pro #5 More money
Because our mudkip is stronger, we require 2 less X Attacks. Funnily enough, despite being slower, we actually need one less X Speed too! Since you don't need one for Tate and Liza either. That makes shopping around 4 seconds faster since we don't need to sell as many things.

But not everything is sunshine and rainbows.

Con #1 Much slower Roxanne split

This Mudkip cannot 2-shot the Zigzagoon it faces. Its defense is too high, and it requires a 1/16 high roll to two hit KO it. You can manipulate this, but for now we will ignore that. Also, our minus Defense nature hinders us here: sometimes you die to Rival 1 + Calvin, and Roxanne and Josh hurt more. This manipulation is also slower than the original (it has lots of room for improvement, though). All of this amounts to around 20 seconds of timeloss, but the route is still faster despite that.

Con #2 Carbos

We need to pick up a Carbos in order to not speed tie Lunatone against Tate and Liza. That's 6 seconds of timeloss, but 8 seconds of timesave against Tate and Liza as a compensation.

Con #3 Worse Archie split

Our defense hinders us here once again: we take lots of physical moves (wing attack and air cutter, sometimes slash) and that makes the Archie split suffer. We also learn protect because we get the Tropius exp from the Winona split, but needless to say that's definitely worth it.

All in all, you will see more deaths during the Roxanne split, but more runs past Wattson and even Norman. Let me know if you have any more questions!