Because the end part wasn't playthru tested by the devs (they had no budget in the end) so they couldn't level enemies properly. So it ramps up in difficulty suddenly.I'm still playing through EB0 on my NES on the stock proto ROM. I don't get why people say it's so hard.
Also, does this uncut version have the crosses fixed? I remember someone was trying to make a similar patch, and the crosses changed tiling or something weird like that.