I never experienced in game the 3.0 darkness spell*, I just know, that it does what its name says: It makes utter darkness - while the 3.5 darkness spell "just" makes a dark area, not completely black.
Because we all loved the idea of utter darkness, we always add a new spell in all our 3.5 campaigns, let's call it "blackness" or "utter darkness". It worked the same way as darkness, but gave the complete 3.0 utter darkness. Darkvision works of course, as does dispelling via higher level light spells. Low-Light Vision etc. does not work.
Spellcaster can choose which kind of spell they learn, maybe the "utter" version is a bit evil-tainted or unused in wizard-schools - if you want to limit its usage.
I searched the web a bit and found a LOT of people using the 3.0 version of darkness in 3.5 - or both parallel - so maybe it will be a good addition to the new game.
(*3.5 was my first D&D - came to it via Paizos DUNGEON and bought my way through the whole program)
I think the cover rules in 3-5 are fine as-is, actually.
I prefer the "everyone is blind" version of darknes. It's wonderful to counter invisibility, blindnes or darkvision in unlit conditions. Not by eliminating your disadvantage, but by creating equal conditions for everyone.
A lesser Darkness works for me too, but I wouldn't want to miss my "sphere of blindnes" :D