First, let's get something out of the way: neither system is really more complicated than the other. Superficially, it seems more complicated: five categories compared to three, right? Except that, as I explained previously, the old system is more like three+two system: Save vs. Polymorph for M-U and Cleric is essentially identical to one of the three main saves, it's just different for each class, and Save vs. Breath for both is almost identical to the Fighter's Save vs. Spells. And for Fighters, Polymorph and Breath are just bonuses to Save vs. Spells. On the other hand, there's really more than three saves in 3e: Fortitude, Reflex, and Will are base categories, but some classes and feats add bonuses to ad-hoc categories, like "enchantments" (druids get a bonus against these, when case by woodland creatures.)
So, really, it's three against three:
- Death/Poison matches Fortitude
- Wands matches Reflex
- Spells matches Will
... except that there's a difference in application. All five of the original saves refer to magical effects (with save-or-die poison being the only natural effect included, as a special form of Death Magic.) Originally, you didn't use these saves versus natural dangers, but instead treated them as simple flat probabilities, unmodified by class or level. For example, there's a d6 save against taking falling damage that isn't modified by class or level: roll 1d6, multiply by 10, and if it's less than or equal to the distance fallen, the character takes damage (this is spelled out in the naval combat rules, p. 31 of U&WA; the explanation of pits in the sample map, p. 5, gives a similar save roll.) The chance of drowning is a percetile dice roll based on armor, not class or level. Traps go off on a 2 in 6 chance. Spikes slip on a 2 in 6 chance. Some things, especially non-lethal effects, get no die roll, but can be completely prevented by appropriate actions. None of these get an ability score bonus by default, although a GM might grant a bonus on a case-by-case basis.
What this means is that a character's chances of surviving everyday hazards are often very high, even at 0 level, and almost certain death (like swimming in mail armor) is always almost certain death, for any level. Saving throws are an exception, not the norm; they give a chance to escape supernatural forces.
In contrast, the d20 system changes everything to one core mechanic: some natural hazards become more dangerous at 1st level, but many also become less dangerous as the character increases in level, because some are based on skills, others on ability checks, but both improve as the character advances -- and some feats add further bonuses as well. Perhaps the fact that all saves get ability score modifiers (and the typically higher values of those modifiers) balances out the fact that first level characters now have a much harder time avoiding drowning in swift water or avoiding damage from a fall.
But here's the meat of the post: the problems with Will. Part of the problem is that a Will save, unlike a save vs. Spells, covers non-magical as well as magical situations, so that you are making Will saves to resist all manner of mental effects that wouldn't even merit a die roll under the old system; you don't have to roll to resist fear, depression, mental fatigue, or any mental effect if it isn't magical, because a character just does whatever the player says.
The other part of the problem is that, with regards to magic, changing Save vs. Spells to Will limits explanations. In OD&D, not every spell is resisted by sheer force of will; some are resisted by luck, or divine favor.
In fact, not every spell in OD&D can be resisted, nor does every resistance require a roll. Phantasmal Forces, for example, can't be saved against (it doesn't affect a victim's mind; it creates a visual projection of a mage's thoughts.) To avoid damage, the character simply has to disbelieve; no roll is mentioned, although many GMs wound up using Save vs. Spells in practice. To dispel an illusion, all a character has to do is touch it.
Also, because Save vs. Spells is now a Will save and is specifically targeted to resist mental effects, spells that don't affect the mind get shunted off into Fortitude and Reflex. What would you roll to resist a magical flash of light that blinds you? In the old system: Save vs. Spells, because you use that for almost everything. In the new system, it depends on whether you consider it an area attack (Reflex) or not (Fortitude.) What about a spell that makes you stink? Spells, for the old system, Fortitude (probably) for the new.
In short, I don't like Will because it changes the way magic is imagined, in ways that I don't want. So, if I were to switch to the three-save system, it would be Fort/Reflex/Spell, not Fort/Reflex/Will, and ability modifiers would not be automatic bonuses, but would only apply when they made sense (Con bonus for poison/death magic, maybe, but never for polymorph; Dex bonus only if the effect is dodgeable and the player says "I dodge".)