I agree that for the vast majority of the levelling process, Mug feels and is essentially worthless (aside from on the free trial, if you're a crafter, and you're trying to level LTW/WVR... ask me how I know...). I'm not sure that making a change that impacts the entire collective of classes is the solution for a problem that only affects Ninja for a limited period of time. In my opinion, Mug should upgrade into a more Ninja-like ability, and have some kind of interaction with the kit -- whether it be keeping the Ninki gain, or something else -- or just be deleted.
You're also wrong in that Suiton -> 5% Trick is a DPS loss for the Ninja. Suiton and Trick (when the rear positional) is hit are both 500 potency each, for 1000 potency together. Assuming we're in single target, the only other combination you'd be expending mudras on is Raiton + Raiju. Calculating how much of a gain a Raiju is is somewhat complicated (it depends on what GCD you finish on), so for the purposes of explaining lets assume Raiju is just a flat gain in potency. So, Raiton + Raiju is 650 + 560 = 1210 potency. This means Trick Attack's 15s duration only needs to gain you 210 potency to break even. Consider that Hyosho will be ((1300 * 1.3 = 1690) * 0.05 = 84.5) an 84 potency gain by itself, I'm sure can you start to see that Suiton + Trick is a huge potency gain, even if all of your teammates decide to stop attacking during Trick.
Assuming you're getting in a Hyosho + two Raiton + two Raiju in every Trick window, 5% Trick will give you 205.5 extra potency from those attacks - +1000 potency from Suiton -> Trick = 1205.5 potency. That's only 4.5 potency away from Raiju, you still have ~6 seconds in Trick Attack left, so even alone Suiton -> Trick is still a gain.
You're correct in that when pugging, relying on people to feed into your buffs to maximise your value is a risk. However, this is true of every class that buffs significantly. Bard and Dancer also struggle with this. The great part about Ninja is that Ninja is very good at taking advantage of buff windows, as it bursts so much in Trick, which lessens the impact. Of course, this relies on your teammates putting up their own buffs on cooldown, but I personally like to assume the best of my teammates, and have a little faith in them. I've cleared all of the "hardcore" content I've done in PUGs, and had a pretty good experience while doing it. You're always going to get teammates you don't mesh with, but that's just the luck of the draw. Sometimes, you'll get a bunch of really great players.
I'm also not convinced it helps progression very much at all, given that Mug is a single-target party buff on a long cooldown. When levelling, you're spending much of your time in dungeons, and very little time in 8+ man content outside of daily roulettes. I suppose you could argue it makes pre-45 dungeon bosses a bit easier? Mug loses a lot of value relative to Arcane Circle, Embolden, Brotherhood etc in multi-target situations like dungeon packs, because you can only slap the one enemy with it. Because most of the levelling content is multi-target, I'm not sure I quite see where the benefit comes in.