BV was fundamentally not designed to handle Zell. It works alright for balancing duels so long as both forces are following the rules, but if you are doing Clan vs. IS then you are going to need to give the Clans something to make up for the restrictions.
I've long agreed with this. Equal BV "assumes" that each playing is going to bring their best, because it seeks to make the sides even in strength and alow skill to determine the outcome. But, if one player is giving up some possible tactics and not bringing their best, then can one take even forces? It is possible, if the Clan player using zell is very good and very tricky, since there are tactics that can make zell more workable or less workable, but mostly I find zell (especaly level 1 zell) to be a disadvantage, and I like for the Clan force to be better than the IS force in such games (that doesn't nessissarly mean more BV, since we all know its deficancies, but a force that an experianced player looks at in the context of pilots and terrain and objectives and says "that's better").
Terrain can also be a factor. As the fluff tells us, lots of broken terrain helps the IS, and open terrain helps the Clans, so they can each engage their chousen opponent at range and just pound the crap out of them. At range against fast mechs, IS return fire won't be much effect no matter which mech its directed against, so zell is a comperitively small disadvantage. But, in broken terrain the IS can lure a Clan mech in a dual into position where several IS mechs can fire at it, while other Clans mechs can not fire at their respective opponents. In a non-zell battle a smart player wouldn't let one of their mechs be lured out like that, but if you're playing very in cherictor and focusing on your duals, its very possible.
Lastly, know all the tricky zell rules. For example, a Clan mech can challange several IS mechs at a time (and why not?) so you don't have to leave seven mechs out when your star engages a company; each can have at least a share of a Clan opponent right from the get go. A mech that breaks line of sight for several turns (two?) can be declaired to be out of the dual. And a few other things that I often forget (but you shouldn't, if you plan on doing it).
Mostly, I only use level 1 zell in early invasion senerios, where I have three or more times the combat power of my opponents and zell is a way to make rolling over my happless opponents more intresting (or, to make being rolled over more intresting, if I'm the IS side).