Hi, I main Bowser, hopefully I can be of help.
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Noa.
Tough guy actually armors based on knockback, not percent. In Ness's case pk fire (the pillar) and dtilt are weak enough to get armored. Dtilt is armored pretty late as well, so you probably should never use it, I believe it gets armored into the mid-late 100s actually. Rage affects this, but generally by the time it works you should probably be trying to pummel -> back throw instead. I'll edit in the actual percent ranges a bit later.
As for the neutral, neither side is really pressured to approach unless the other sidre has a lead. Pk thunder is slow, lacks priority, and easily perfect shielded. Pk fire lacks range for a projectile, lags significantly, is very small, thus easier to avoid, and is woefully telegraphed. It's very possible to punish on reaction if the opponent is ready.
On the other hand, Bowser's furthest reaching attack is neutral b which lags somewhat and can be absorbed. So the neutral between both characters can be really tricky and, in my experience, usually boils down more to a mental game than anything else. Both sides can get blown up if they go aggro.
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EnhaloTricks
Since you may not be used to playing that kind of neutral, while your opponent was, it's entirely reasonable that you'd lose in that scenario. Doesn't mean you're bad, just means the other guy played the match-up better.
I'd offer to play you, but I lack the means to play online at the moment. However, the folks over at the Bowser boards are good people, so if you ask for some pointers in the match up thread I'm sure someone will help you out.
Hope this helps, good luck!
EDIT: Tough guy percentages.
(Regular Armor)
PK Fire (Pillar): 0-44% Basically every hit after the initial one.
Dtilt: 0-164%
Lasting PK Thunder - Up B 2 (Tail): 0-104%
(Armor + Crouch)
Jab1 14-41%
Jab2 14-41%
Dtilt 164-209%
Lasting PK Thunder – UP B 2 (tail): 105-150%
Unfortunately none of this data factors rage or move staling. It was all tested in training mode. However, these percentages should be largely accurate.