The official HBase doc suggests one Colum Family is best for performance. Tow or three could lead some performance problem. Above three ,it is a design flaw leading a big performance problem.In another words, one table with 3+ column families can not happen in production environment. I think it's big disadvantage compared to Goolge BigTable which allow 100 column families.
And compaction algorithm has many version, I guess HBase guys could not find the right algorithm.The algorithm is key to the performance.Why not ask help from Google guy?
The second edition of HBase definitive guide is due to July this year, hope it can do better job than HBase official doc.