I was going to post in the other illusion thread, but this one fits a bit better...
I never really had a chance to play a 1st ed Illusionist, though I know they were fairly different. I do think that an illusionist has gotten a boost between 2nd and 3rd editions, based mostly on their denied schools:
In 2nd ed, the illusionist was forced to lookse Abjuration, Evocation, and Necromancy. There were the only specialist that lost three schools, and got the least in return. Also, as someone pointed out in the other thread, there was a ton of stuff in 2e that was immune to illusions. During the campaign I played in, none of my illusions would work on any undead, outsiders, or just about anyone with infravision (unless I used the higher-level spells that could do thermal components). It may have been house rules of my DM, I don't know. At least he didn't do automatic disbelief saves.
In 3rd ed, illusionists only loose 2 schools, and they can pick which ones. Also, there's the universal school (taken from the Options books, I think), which I'm quite thankful for. Under 2nd ed, being barred from abjuration meant I lost things like "dispel magic", which I consider a pretty standard spell for any mage. I often complained that my 15th-level illusionist could frighten people to death with a gesture, but couldn't dispel a "hot foot" cantrip cast on him by a peasant apprentice.
So I guess, really, between the editions the illusionist was brought in line with the other specialists. Now, as for 3.0 vs. 3.5, I haven't looked to closely yet. I always had a house rule that disbelief wasn't automatic, and took a standard action, so no news there. As for the invisibility spells, well, it does sort of take the deception/stealth aspect out of them. I can only assume they were toned down for the "scry and fry" crowd that likes to use heavy magical ambushes- it seems like a lot of 3.5 changes were made in response to these tactics. The durations would be a small thing to house rule, and it would require less changes than I wanted to make in 3.0
The Spellcraft thing is interesting, as I hadn't thought of it and it never came up in our games, even with a PC illusionist for a couple of years. An idea I had while reading it was to give each specialty school a unique skill, possibly in lieu of Decipher Script if the DM is so inclined. Illusionists would get Bluff as a skill, and could use it to disguise what they're casting- they mutter the words and make subtle and misleading gestures.
Since we're already venturing into House Rule territory, here's a possible list of skills:
Abjurer: Use Magic Device
Conjurer: Diplomacy
Diviner: Sense Motive
Enchanter: Gather Information
Evoker: Intimidate
Illusionist: Bluff
Necromancer: Heal
Transmuter: Disguise
These are just off the top of my head, I'd be interested to hear any suggestions. Oh, BTW, there was a feat called "Spell Thematics" in one of the FR books that did make it more difficult to identify the caster's spells, I think it raised the DC by +5 or something.