I actually disagree with with some of these 1h points, but we may just use different tactics.
I find the best way to deal with a agi-ninja is to use a shield and a fast 1h. I use a Heavy Heater Shield (not the fastest by far) and I find that super-agi doods usually have lower PS, so I don't really have to worry about them breaking my shield. So I let them spam away until A) an opening is created, B) I can shield bash them and make an opening, C) a teammate comes behind them and whacks them.
I will concede two points though. First, it's only been a day since the patch so maybe I haven't faced the same types of builds as you. Also, the super agi builds ARE difficult to fight. Whenever I encounter another sonic-speedo with an estoc, I give a heavy sigh and march in, shield raised...