Yes, I think new version is much easier. I think two items have to be nerfed:
1. Homing Phase Device. It's easy to skip at least 2 levels (I usually have 2 HPD by dlvl20), maybe more if stairs are generated nearby - i don't use HPD right away, I check the nearest rooms for ammo/powerups first. I have two ideas for this item: you have to spend some time on the level before using it (worse idea, because you may skip that time by walking inside closed room) or you have to reveal certain % of map before using it (the percentage may be different for different level types - it's easier to reveal map on "arena" or "cave" level than "labirynth" or "bunch of small rooms").
2. Armor Durability Mod. I'd change it to 150% max, x1.5 current durability when used.
I probably haven't found any uniques, because after I got BFG I didn't clear every level. In my Avatar of Purity game I found Minigun, but it sucked for me (I didn't have EE and SotB and it's accuracy was very low) and in Hurt Me Plenty game I found Missile Launcher, but if I remember correctly it was worse than my modded Advanced Rocket Launcher, so I left it.