Thunderforged items were a terrible idea to begin with, causing even MORE gear disparities between 10 and 25 man. Its wasnt nacessary to have a higher TF drop rate in 25 man raids (10% vs 25%), because they already get a higher chance for TF items, since 25 mans drop more items (2 vs 6). So this causes them to double dip... higher TF drop chance + more items.
I always monitor people who play the same classes as me, but are in more progressed guilds... the first thing you notice is item level of 520 vs 530+ on some of them. One solution to fix this, could be, that you wont be able to upgrade your TF items, but rather let your normal or heroic item be upgradable to TF quality.