I think PGI wanted to just do it as we see will happen, an even skill tree for both IS and Clan. Result would be as they hinted at, WILL kinda make Clan better overall.
Solution could be either nerf the percentages on Clan nodes, but also remember there ARE Clan mechs suffering just as much as IS mechs. Then, nerf/ buff individual chassi as needed to even it all out.
I'll try to explain it better. For example buff percentages SLIGHTLY for IS nodes, buff the "weakest" mechs chassi ( Vindicator, Jenner, Victor, Cataphract f.ex) variants individually.
At the same time buff the individual mech chassi configs/podsfor the Clan mechs that struggle. Say the Summoner, Mist Lynx, Gargoyle. OR nerf the overperformers nodes for say.. Kodiak, Mad II.
Really, the Clan II mechs seems to be stronger than their Omnimechs in some regards, that isnt right, I know its PVP but still Clan OMNI and Battlemechs should be at LEAST side grades to each other. Kodiak and Dire Wolf, Warkahk and MAD II should be both be viable. This coming from a IS loyalist piloting salvaged clan mechs