uh, there's three questions, but you can only select one option...

2. No: i don't want to alternate all cobra and all joe drafts every other game.
3. Yes: i want a round robin tourney where everyone plays everyone one time, and the teams with the most victories advance to the next round.
5. Yes: i want named cobra and joe leaders excluded from scenario stories

that would be my answers.

I would like to mix things up but not necessarily every other game, maybe just once every third or fourth game to prevent things from getting too stale.

I don't like to have any named characters in the missions because it complicates things regarding factions and how that character would act as interpreted by the player.

Having a made up enemy is much better. Players have no idea how they would act and it makes them think more about possible scenarios.
It is ok to have standard troops in a mission that makes sense.
night creepers in a dojo sand scorpions in the desert etc etc.

and now I have to go google" round robin tourney."

We did a round robin long ago. It was where I made up brackets and such. Im down with that again. Im also for exluding names from specific missions, however, I think Skinny has the better approach.

Whatever you guys want to do im cool with .Does it have to be one or the other? Maybe just alternate one gameall cobra/joes and the mixed again?

My vote....

No
No
No

leave it be, or at least let proto win a tourney once i think ive been to the finals in almost every round what gives you'd think id win at least once right?

Hagaha proto i've never won either but truthfully i enjoy being able to draft both cobra and joes on my team, thats half the fun why are we changing the game?