You're right. For a project that has this much new stuff, I probably should have included an explanation. I guess my subconscious thought I'd already typed one up, because I've explained it to playtesters and folks here on the ENBoard several times. So, I'll put up an official compilation of explanations, and make sure to include it in the sequel book.
As to your question, it was part flavor, part balance, and a lot of ease-of-play.
For the flavor, I knew the spell lists give you a lot of flexibility, and in combat, when time is tight, you might be tempted to min-max and use just the right spell for the situation, with precisely the right area, range, and so on. But because combat is where a lot of cool, dramatic stuff happens, it tends to become a big part of the history of your characters. I like it when spellcasting characters have spells that they use over and over; it gives them personality. So by encouraging people to use signature spells, it makes your magical 'fighting style' more distinctive.
Also, with signature spells, you'd feel less pressure to have tons of options available in combat, because you'd be content with a few well-designed spells you prepare in advance. This frees up characters to devote more spell lists to a particular motif, and less to the 'sorcerer syndrome.' I'm sure you've seen a couple threads where people bandy about what the 'optimal' list of spells known is for a sorcerer.
For the balance, it's again much the same problem -- too much flexibility making Mages with a good spell selection very effective. You can still take your time and have flexibility when you're not in danger, but in combat you've got less time to think of what's the best thing to do. I hoped this would be a happy medium between 'utility wizards' and 'blaster sorcerers.' Because Mages do still have a bit more flexibility even with the signature spell restriction, you'll notice their spells are slightly less powerful than what's available at the same level for core spellcasters.
Also, this emulates the sorcerer restriction that metamagicking a spell takes a full round.
Finally, and most importantly, for ease of play. . . . In one playtest, where a 20th level mage and a 20th level fighter faced off against an array of random monsters (including a tarrasque), the fighter's turn, even with four attacks and some number crunching to finagle out an effective power attack, took about a minute and a half. The Mage's turn, after he used Create Time to spend a few bonus rounds buffing himself and the fighter, then summoning monsters, then casting a weaker quickened create time to get one spare round then transmuted the floor under the tarrasque to mud, and ended with a 20-MP Evoke spell touch attack cast through an unorthodox usage of Move Space, took about 10 minutes.
Without the signature spell rules, spellcasters can take a long time creating spells on the fly. Even with a one full round casting time (the original time when casting a spell on the fly), it didn't deter many people, particularly when they had meat shields to keep them safe as they cast. A two-round casting time means concocting a spell mid-combat will keep the player busy for a while, during which time the rest of the group can continue on with combat.
Also, signature spells make NPCs easier for GMs to come up with. That's actually the biggest hurdle with adopting this sytem, because GMs usually won't want to slow down the action to come up with a complete spell for a mage villain on the fly. Players at least can think when it's not their turn, but GMs are always busy, so signature spells encourage a bit of advanced planning. And ... *cough* if you ever sort of stuck for ideas, you can just 'double check' the rules and make up a spell on the fly, but assure your players it was a signature spell.
Actually, I was hoping people would be interested in coming up with a bunch of example spells, so we could have a web compilation of possible signature spells. I think it'd be a nice resource for GMs, and it could impress players by showing them what kinds of nifty things are possible with this system.
Now, the logical result of the signature spell rules is that your signature spells will end up being your 'combat spells,' or rather 'action spells.' I don't really see a problem with that. You can still have a nice variety of 'action spells' that aren't all evocations -- one mage has been getting a kick out of creating tons of weird wall spells that let him change the battleground.
Any other questions?