The Rogue, a bully

 The Rogue and Grisou are the same age, neutered on the same day and grew up together after that. Somehow the Rogue grew up to be 20 lbs, while Grisou remains a lean 11 lbs. Needless to say, a wrestling match doesn't end well for Grisou. He used to escape to the highest cat tree (that the Rogue is to fat for), but once he discovered the cat flap to the great outdoors, he runs there. Now I know the Rogue isn't necessarily mean, just bored and likes if anyone runs from him. He has other playmates who either don't mind the wrestling or scream indignation at the top of their voice, but still can't resist to try tackle poor little Grisou.

There are toys, lots of. There are separate feeding stations. There are cat trees. There's the yard, with the unlucky lizard or butterfly, and other cats. We started clicker training and are as far as the click is associated with a treat, which doesn't help any with the Rogue's bullying. Whenever I notice the Rogue to start targeting Grisou, I try to distract him (but am concerned that this would reinforce the bullying!).

Once I caved in and gave the Rogue a timeout, 5 minutes locked in the bathroom until he started crying (I did, of course, feel terrible). I'm not sure negative enforcement works with cats in general, or the Rogue in particular, who is generally unconcerned about anything, least of all me saying "NO" in a determined tone of voice.

Any thoughts on whether or not timeout is a tool for misbehaviour? Any advice on the bullying?

I'm unconvinced that timeout is an effective tool for cats, unless the cat has almost lost a sense of where they are and needs time to decompress. That doesn't sound like the Rogue to me!

Have you tried focusing on building Grisou's confidence with daily interactive playtime (especially mimicking the hunt-kill-eat cycle)? I kind of get the feeling he's at the bottom of the pecking order, and may be acting the most like prey. As far as cats are concerned, if you act like prey, you can expect to get treated like prey! 

Daily interactive play for the Rogue might help wear him out and give him less energy to beat up his brother (it might also help with his weight too).

The other thing that might really help is Spirit Essences - I think theres one for bullies (Rogue) and one for victims (Grisou). I've had great results using flower essences on my animals - its got to be worth a try!

Clicker training is great, but it may not be wonderfully helpful in stopping the Rogue's antics. You can train a really solid sit-stay and a leave it in a dog, but I'm skeptical as to how far it could be taken in a cat. Sit is no problem. Sit when you've homed in on your prey of choice.....not so much (imo, anyway). I know how hard that is to achieve with a really determined off leash dog...and dogs want  to please you!

I'm sure you've read these already, but just in case:  [article="29678"]Cats And Discipline Dont Mix​[/article]  ;  [article="32493"]The Dos And Donts Of Cat Behavior Modification​[/article]  ;  [article="0"]Cat Play The Rules Of The Game​[/article]  ;  [article="0"]Playing With Your Cat Ten Things Every Cat Owner Needs To Know​[/article]  

Thanks for the advice, you're so right!

Grisou is acting as prey. It usually goes like this: Grisou wants to cross a room, notices the Rogue, starts to growl. The Rogue, intrigued, starts running towards him, which in turn gets Grisou running like a rabbit with its tail on fire, the Rogue right behind him.

If only my Grisou would stand his ground! Everyone else does, even Geronimo, who is Grisou's size and plays with the Rogue all the time.

As it's not possible for me to wear the Rogue out, I have to work on boosting Grisou's confidence. It can't be that bad, this is someone who can capture a gopher and drag it through the cat flap right into the living room for everyone else to admire.

So I'll do some research on how those spirit essences work, and wave all the wands around.

Good luck! 

so, for boosting Grisou's confidence:

he is already fed before everyone else (if he shows up, that is), on a place higher than the common feeding place. The other guys get all of his leftovers.

His favorite resting spots also are high up.

I did research the flower essences and couldn't find any evidence that they are better than placebos... so I'll save some money here.

Does anyone have any more recommendations on how to boost a cat's confidence? 

I understand your skepticism about flower essences, but I've seen them work time and again with my animals - cats, dogs and horses. They're not miracle cures or magic bullets, but they can and do tip the balance in your favour when trying to alter behaviours. Believe me, I'm a skeptic too, but I tried them out of desperation on a very emotionally damaged horse I had and they really helped. Just my