Ok, here's the problem. The real problem.
The problem here is that 80% of clan designs can basically be defined as shit. The other 20% are good, some of them very, very good. Most people tend to only use the very good ones, some more the good ones, and very few the bad ones. There's also very, very few mech designs by clan that are simply ok, they either suck or are amazing.
Second of all, the clans are almost always outnumbered. They have high BV mechs that require higher level pilots, which shoots the cost up even further. So basically, clanners are almost always numbered, usually pretty badly.
The clan's strengths are about long distance fighting, superior movement and superior marksmenship. Basically, clanners fight better at range and with harder shots. They get ruined up close, where being outnumbered is a huge disadvantage.
So the clan strategy is one of denial, dancing at long range taking semi pot shots at the IS mechs. A really good clan player can dance like this all game, basically preventing the IS player from ever getting close.
This is of course frustrating as shit for the IS player, who more than likely plays IS because he likes a good brawl. So he cries cheap and bullshit, even though it's simply a matter of the opponent being more skilled then him. Meanwhile, if the IS player is superior, he swiftly closes the range and the clanner gets royally fucked.
IS vs IS is a balanced matchup where both players get their desired style of play. Clan vs Clan is the same way.
IS vs Clan has all sorts of balance problems, some people make out bigger than they are, but the problem is conflicting playstyles.