I dunno, if there are innovative ways to design the game around the concept of clan tech being better and yet still be able to balance the game I think it would be cool to have them be different.
All the way up to Heavy the IS and Clan are pretty evenly matched because the IS has had time to catch up in this timeline, but clan assaults are supposed to be big and badass. There are ways, look at Zeus' system, hes coming up with creative ways to use the economy as balance, there are ways to make it work if the devs are willing to spend the time on that particular aspect.
I think it would cool to have them be different as well. NOT BETTER. I don't care what balancing is done, if one team has better mechs, regardless of the hurdles required to get them, that team is going to attract an excessive number of players. Clan assaults can be big and badass. IS assaults should be big and badass too, or noone will want to play IS. They should be EQUALLY big and badass, in a DIFFERENT way. I'm not suggesting homogenization, as noone wants the sides to be the same, but you should not be able to describe one side as "better, but balanced by x".
Personally, I think some great ideas have been brought up, especially along the lines of using various mechanics to make the IS mechs more "hardy". Maybe not necessarily more armor, but perhaps less affected by splash (Can be explained by less streamlined designs), less critical effects due to the bulky design, etc. There are a lot of more imaginative ways to balance than the obvious variables, and I really like that direction.
In the end, the answer for me shouldn't be "Well clan mechs are better so
x". Seems to me some people are so in love with the clan and the idea that the clan is
simply better, that we have to get beyond that idea and help make a game that's fun and has a draw to join both sides.(As much as blithering on the forums and playtesting an awesome mod is
helping) Being the underdog can be fun, but it's definitely not a positive trait.