To beat the early stages you should have at least level 30 or 40 champions in lifesteal gear. To beat the first boss you're probably going to need at least 1 good level 60 and some good level 50's.

RNG plays a large role in winning battles unless your champs are well, well above the power required to beat a stage. If you won in close battles, upgrading gear still might not be enough to put you over the threshhold for 100% victories.

Also, there are lots of other things that can change with the team makeup as you upgrade gear. For example, upgrades can increase speeds, changing the order your champs go in, sometimes causing an AoE decrease defense champion to go after your DPS champs. 

If you need some particular specific help, go ahead and post some screenshots of the stage you're having trouble with, and the team you are using, and we'll see if we can make some suggestions. :)

The OP said

If a given team beats a given stage it should ALWAYS do so.  (paraphrasing obviously)

RNG much?

Far more important than anything else is - stop wasting your time on faction wars. I'm making an assumption, but based on your question, I would hazard to guess that you are relatively early in the game. Faction wars is endgame content. You will seriously cripple your ability to progress if you start wasting resources on sub-standard champs just to advance through FW.

While i think a good dragon team and a good clan boss team are the most important factors, i dont think people should ignore faction wars personally

The perception gear you can get as a result is better than many can get from dragon runs.

At the state of progression the OP is in, it is very likely he is leveling sub-standard champs for FW. Things like uncommons or possibly even commons, just to be able to make up a team. That is hugely wasteful. Even rare champs are likely to be a massive waste of resources when he needs to be focusing on getting useful champs to 60.

As long as the sub-standard champs are not levellled to 60, there is no problem in levelling them. They can serve as food later on. Just don't waste to much resources (energy for Mino runs, silver for gear upgrade) on them. Artifact level 8 is a good compromise between silver cost and gear quality.

I just chose which champs I saved from my food leveling based on which FW crypt was coming up. This way I could run those crypts before fooding those champs.  You can at least run the first couple levels every day, and don't sleep on how good that 4 star perception gear can be for an early game account. :)

Level up food, throw on some okayish gear, run the the levels. If my memory serves, I made it all the way through the first Banner Lords FW boss with Rowan and Dagger carrying me, perception + lifesteal, and a small army uncommons, mostly Commanders. lol

Several  Questions must  be  asked  &  answered  in  order  to  find  the  correct  solution.

1  -  What  Faction  are  we  talking  about?

2  -  What  Faction  Stage  are  we  talking  about?

3  -  What  Heroes  are  you  using  in  the  Stage?

4  -  Who  are  the  enemies heroes  you  are  fighting against  in  wave  1?

5   -  Who  are  the  enemies heroes  you  are  fighting against  in  wave  2?

6   -  Who  are  the  enemies heroes  you  are  fighting against  in  wave  3?

If  you want  help,  you  have to  provide  the  above necessary information.

Otherwise,  it  is  impossible to  know  why  your  not  winning.

If  you  don't want  help,  I  will  provide  you  with  Background  Music  to  compliment your  whining.

 Just  vent  out  all  your  frustration!

Here  is  a  Music  Video  -  60  min's  of  the  Sad  Voilin.

It  is  fitting  that  I  chose  a  Violinist  song  to  compliment your  situation.

Your  Faction  War  team  is  sinking  just  like  the  Great  Ship  named  the  Titanic  and  the  Violinist  will  play  on  till  the  bitter  end.