PS2 version is bad because it doesn't have a progressive scan mode. I have component cables but I still have to put up with interlacing which throws my game off.
PC version runs at 60 FPS progressive scan. Exact frame timing? No problem!
If you're talking about HDTV lag, you likely still have HDTV lag coming from your PC, even though it's progressive, because it's not scaled to your TV's resolution. Melty Blood runs in 640x480, which scales to a standard def TV as 720x480(non-square pixels). Either way it's a lot lower than a HDTV resolution, so it'll likely still lag...but not as much as an interlaced signal will.
If they do a ps2 release, I hope they include a progressive scan option. At this day in age, it's harsh to do ignore that.