Oh, did you also just come back from a break as well? A few months ago I altered the animations so that isn't the case anymore. You might die .1 % of the time in a duel due to the two-handed animation reaching its sweetspot a full 1% faster than you. Just two days ago I took another look at thrusts, what I found, is that the 2h thrust is now the least optimized out of all of them. Of course, I think that makes balance better rather than worse since they have the best range and are conveniently head level.
As far as being able to hit LATER in the animation... that's a new one that, because it's basically inconsequential for balance, has been ignored. I can take a look at the animation later today and say objectively whether or not that is the case. Even if it is though, it will be heavily dependent upon weapon speed in such a way as to only matter for the slowest of two-handers.
No, I've been here the whole time, unfortunately, and have yet to see any major improvement to polearms, save for the overhead. Even that is only really noticeable on the really long poles, generally the 2-directional ones. You even said yourself that the right-left or left-right (one of the sideswings) was a little slower for poles and yet left it untouched.
In addition, you acknowledge that there is still a 1% difference... you can't say that they are the same / balanced until there is a 0.% difference.
Optimization =/= effectiveness. Maybe the 2handed stab is OP because it is so poorly optimized. For example, if the animation actually thrusts for .05 seconds, but the active period lasts for .15, that is not optimized at all, yet it helps the 2handed stab. The old 1handed stab wasn't optimized... its effective duration was before it should have been. It was useable, but took some getting used to. Now that it is optimized, it is effective and works more logically. If 2handed stabs were optimized then maybe they couldn't stab point blank AND at the far end... just during the time the sword is actually extended*.
*note: 2handed stabs always seemed to be the "most realistic" as far as active time is concerned... they thrust forwards quickly, and are effective early in the animation... makes sense. The only problem with the animation/activation stage is in the end... where 2handers can spin around and catch you with the end even if they completely missed you at first. When you optimized the 1handed stab, it started behaving more like a 2handed stab, and nowadays is essentially the same exact thing just on a shorter scale. Now that 1handed stab 'is optimized' and behaves exactly like a 2handed, you say 2handed stabs AREN'T optimized...