1st: At the time I thought the T-1000 was too fantastic to be believable in the real world. Now they actually have chemicals that can make shapes with eletromagnetic stimulation. So, that's actually a check in the minus column that has been erased.
2nd: It ruined the circular timeline that T1 set up which indicates that John would not have been born if Skynet hadn't tried to keep him from being born, and that Cyberdyne would not have developed the tech without the T-800 remains in the factory. The events that lead to those two things happening involve Judgment Day happening on August 29th, 1997. When the events of T2 happened, that timeline was altered, and thereby could not possibly yield the same course of events that culminate in the 1984 time incursion. Logically, every person that would have survived the War starting in 1997 would now be in a different place with the new J-Day event, so all bets are off on who survives at all.
3rd: Arnold was supposed to be the exact same model as the T-800 model 101 in T1, but he looks smaller and older. Yes, I know the actor aged and there's zip that can be done about that, but it kept me from believing the character as much. But that's just the visual which I can live with.
4th: Arnold played the Terminator WAY too human in T2. Thank God for the Special Edition which shows the CPU switched from read only to learning mode to help make some of his antics plausible. Even so, I just had a sense that Arnold knew his character was cool, and so did James Cameron, which is why they played "Bad to the Bone" when he got on the bike. Absolutely it was a cool scene, but the worst thing you can do to a cool character is tell the audience that he is cool. The biggest thing that pissed me off is after Arnold grenades the 1000 off the platform, when he stands up as though humanly exhausted and says, "I need a vacation." WTF! There was no logical reason for that comment except to get a laugh. Lame. The constant humanizing of the T-800 just because he was the hero ruined the image of what a Terminator is, even if it's reprogrammed, and there was nothing of the T1 Terminator represented. In that regard, I thought he was more believable as a Terminator in T3, even with the stupid lines. At least there were logical reasons for the dumb stuff he said. Things like "Talk to the hand" was because the stripper said that to him, and "I am not ____ting you" was a direct response to Connor's accusation.
5th: As mentioned above, the skin healing issue. In the first movie, the wounds rotted. That's what I would personally expect from a machine wearing flesh as a disguise. It's not eating, so where is the new flesh material coming from to heal. It's a disguise like clothes. They get ruined, you get new clothes. A Terminator uses its skin to infiltrate, not play bodyguard for 150 years. After target is terminated, it goes back to be reskinned for another mission or it becomes a foot soldier like we see at the beginning of T2.
6th: The difference between practical and CG effects on the T-1000 was so obvious that it was hard to suspend disbelief.
7th: The huge budget (for the time) and the excessive actions scenes, while entertaining to watch, eliminate the realistic, gritty feel the first movie had which keeps me thinking I'm watching a very polished action movie instead of something completely believable like T1 or movies like Predator and District 9.
I can go on...
