I noticed you are only playing 40 minute games. That's going to help with his stamina.
For those guys he plays, maybe he has a bruiser type team which wear opponents out. It's hard to say without looking at the roster. I've played teams before where I'm like why are my guys so tired when they wouldn't normally be so I've seen it happen. Could have something to do with the schedule in the my league too. Scheduling might make guys more tired in the coding. I don't know.
That being said, I think I could go a whole 48 minute game without a timeout. A lot of guys do that surprisingly and it doesn't affect gameplay. If he's subbing that's the most important thing. Timeouts, while I like to see them called are there mainly to generate ad revenue in real life for the most part with exceptions for certain situations. Usually the other guy will call timeouts and that's all the rest you might need.
Some guys save them up towards the end and call two or three in a row to rest up which is annoying.
If you have made him an admin of your league or he made the roster to begin with, he could be cheating but if he isn't I doubt it.
I am not a big fan of rules for gameplay. Most are in place to help people play defense. Yeah PIP can be high, but if you limit it, then people can just press you all game on the perimeter knowing you have to limit yourself. In reality, ALOT of people I play, press the perimeter all game and then they are just asking for it.
I also think that, fast breaks can be stopped with better shot selection on offense. If you limit fast breaks off missed baskets, there's no penalty for poor shot selection.
Best rule in today's world for leagues is suit up and play no matter how the other guy plays and just let the commish keep an eye on the playstyles and eliminate guys that get on guys nerves.
If I were to make any rules, I'd make them about defense and not offense because that's where all the crap is. Zones and presses with wonky defensive settings just kill the game in my opinion.
I know you didn't ask for my philosophy but some guys know the game well and you can give them any team and they'll kick people's butt with it.
Just the way it is.