I like the new changes as I have a red/green colorblind. It's mild but the new system is much easier to see.
I don't see how the pulsing is throwing off peoples timing. A big colored spot is a big colored spot. Whether it's pulsing or not is fairly irrelevant. Timing with these things has always been annoying since so much of it is server side and latency affects it. As far as I know that hasn't changed.
It's just a matter of getting used to it. Since most men have at least a slight degree of colorblindness (if they realize it or not) this change is kind of necessary to keep the purpose of the tells in game clear. Everybody adapted to the inaccuracy of the telegraph, they'll adapt to the pulsing easier than that.