Actually though, just using this example, toughness isn't all that bad. Effectively, most PC's are operating 1 hit die higher in hit points. Ok, toughness for a Barbarian is bad, but, I'm fairly confident that most people can clue into that one. However, toughness for a sorc or mage at 1st level isn't a terrible choice.
Besides that, that's what the learning curve is all about. If I took proficiency bec-du-corbin in AD&D, that would be pretty much a waste of time. It didn't take a whole lot of time, but, there was still a learning curve that Prof-Longsword was the way to go.
For a complete newbie, what's wrong with handing them the pre-gens? It gets the job done and they're playing very quickly. One of the big points for 3e is the fact that players are meant to have some input outside of the game. They are meant to take the time to read the PHB and, yes, buy a Complete book as well. The retraining rules in the PHB 2 take a lot of the sting out of bad choices, but, honestly, our group had been using something similar for years. If you took a NWP, or a skill/feat (depending on edition) and never used it, most DM's including myself, IME, would let you switch it out for something that fit better. To me, the retraining rules simply codified something that a number of groups had been doing all along.
Let's be honest here. Beyond Basic/Expert, D&D has never really been a casual game. There are areas in all editions that were complex. AD&D's combat system wasn't particularly easy - space requirements, initiative rules that were arcane, proficiencies, unarmed attacks, weapon vs armor tables and a host of minis based rules like shield facing and flanking rules etc. 3e has some pretty rough patches of complexity as well. Chargen in 3e is more complex - there are more choices and many of the choices have consequences that will come back time and again.
I'm not sure if that's really a difference between editions. The places of complexity may be different, but, the level of complexity isn't all that different overall.